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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 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy

The photochemical reaction pathways of CHBr3 in solution were unveiled using two complementary X-ray techniques, time-resolved X-ray solution scattering (TRXSS) and X-ray transient absorption spectroscopy, in a wide temporal range from 100 ps to tens of microseconds. By performing comparative measurements in protic (methanol) and aprotic (methylcyclohexane) solvents, we found that the reaction pathways depend significantly on the solvent properties. In methanol, the major photoproducts are CH3OCHBr2 and HBr generated by rapid solvolysis of iso-CHBr2-Br, an isomer of CHBr3. In contrast, in methylcyclohexane, iso-CHBr2-Br returns to CHBr3 without solvolysis. In both solvents, the formation of CHBr2 and Br is a competing reaction channel. From the structural analysis of TRXSS data, we determined the structures of key intermediate species, CH3OCHBr2 and iso-CHBr2-Br in methanol and methylcyclohexane, respectively, which are consistent with the structures from density functional theory calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Unsupervised machine learning discovery of structural units and transformation pathways from imaging data

We show that unsupervised machine learning can be used to learn chemical transformation pathways from observational Scanning Transmission Electron Microscopy (STEM) data. To enable this analysis, we assumed the existence of atoms, a discreteness of atomic classes, and the presence of an explicit relationship between the observed STEM contrast and the presence of atomic units. With only these postulates, we developed a machine learning method leveraging a rotationally invariant variational autoencoder (VAE) that can identify the existing molecular fragments observed within a material. The approach encodes the information contained in STEM image sequences using a small number of latent variables, allowing the exploration of chemical transformation pathways by tracing the evolution of atoms in the latent space of the system. The results suggest that atomically resolved STEM data can be used to derive fundamental physical and chemical mechanisms involved, by providing encodings of the observed structures that act as bottom-up equivalents of structural order parameters. The approach also demonstrates the potential of variational (i.e., Bayesian) methods in the physical sciences and will stimulate the development of more sophisticated ways to encode physical constraints in the encoder–decoder architectures and generative physical laws and causal relationships in the latent space of VAEs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in Neurospora crassa

Significance Microbes have evolved complex signaling networks to identify and prioritize utilization of available energy sources. For many fungi, such as Neurospora crassa , this entails distinguishing between an array of carbon sources, including insoluble carbohydrates in plant cell walls. Here, we identified a repressor of the cellulose-response pathway in N . crassa . Using this derepressed mutant, we implicated the conserved hyperosmotic-response MAP kinase pathway in regulating the response of N . crassa to insoluble carbohydrates. We hypothesize that fungal species that degrade plant biomass use osmolarity as a proxy for soluble sugar in the environment to regulate their nutritional responses, enabling tailored production of lignocellulases. This finding could help in battling fungal plant diseases and in the production of second-generation biofuels.

Huberman, Lori B.↗
DOE OSTI2018

Eigenvector centrality for characterization of protein allosteric pathways

Determining the principal energy-transfer pathways responsible for allosteric communication in biomolecules remains challenging, partially due to the intrinsic complexity of the systems and the lack of effective characterization methods. In this work, we introduce the eigenvector centrality metric based on mutual information to elucidate allosteric mechanisms that regulate enzymatic activity. Moreover, we propose a strategy to characterize the range of correlations that underlie the allosteric processes. We use the V-type allosteric enzyme imidazole glycerol phosphate synthase (IGPS) to test the proposed methodology. The eigenvector centrality method identifies key amino acid residues of IGPS with high susceptibility to effector binding. The findings are validated by solution NMR measurements yielding important biological insights, including direct experimental evidence for interdomain motion, the central role played by helix h α 1 , and the short-range nature of correlations responsible for the allosteric mechanism. Beyond insights on IGPS allosteric pathways and the nature of residues that could be targeted by therapeutic drugs or site-directed mutagenesis, the reported findings demonstrate the eigenvector centrality analysis as a general cost-effective methodology to gain fundamental understanding of allosteric mechanisms at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A small single-domain protein folds through the same pathway on and off the ribosome

In vivo, proteins fold and function in a complex environment subject to many stresses that can modulate a protein’s energy landscape. One aspect of the environment pertinent to protein folding is the ribosome, since proteins have the opportunity to fold while still bound to the ribosome during translation. We use a combination of force and chemical denaturant (chemomechanical unfolding), as well as point mutations, to characterize the folding mechanism of the src SH3 domain both as a stalled ribosome nascent chain and free in solution. Our results indicate that src SH3 folds through the same pathway on and off the ribosome. Molecular simulations also indicate that the ribosome does not affect the folding pathway for this small protein. Taken together, we conclude that the ribosome does not alter the folding mechanism of this small protein. These results, if general, suggest the ribosome may exert a bigger influence on the folding of multidomain proteins or protein domains that can partially fold before the entire domain sequence is outside the ribosome exit tunnel

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ 0 and preQ 1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ 0 and preQ 1 , the enzymes and transporters involved in Q salvage and recycling have not been well described. In this work, we discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis , uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile , salvages preQ 1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Freeze-induced crystallization: An overlooked pathway for mineral genesis in natural waters

Natural ice plays salient roles in making the Earth habitable and sustainable. Previously overlooked, its role in chemical processes is now of emerging interest, particularly due to the freeze concentration effect, which can substantially promote chemical reactions during ice formation. We demonstrate here that ice formation can serve as a dynamic and unique pathway for mineral genesis. Freezing solutions containing dissolved manganese and carbonates produced rhodochrosite (Mn II CO 3 ) even under slightly undersaturated conditions. At room temperature, by contrast, this occurred when the solution saturation level was increased by ca. 30,000 times. The cryogenic rhodochrosite formed spherical aggregates of nano-polycrystallites, distinctly different from the cubic monocrystalline particles observed at room temperature. The distinct feature likely resulted from the combined effects of the intensified supersaturation induced by the freeze concentration effect and the low temperatures within liquid-like layers, conditions that make liquid-like layers an exceptional environment for mineral genesis, unlike typical natural water systems. The cryogenic rhodochrosite formation was successfully demonstrated using in situ, real-time X-ray absorption spectroscopy (XAS), enabling direct observation of freeze-induced solid formation. In conclusion, our findings reveal that freeze-induced crystallization may be an active mineralization pathway, potentially influencing elemental cycles within the cryosphere and contributing to minerals with distinguishing properties and reactivities in the environment.

Earth, Atmospheric, and Planetary Sciences↗
DOE OSTI2025

Multistage nucleation pathway in LiF molten salt mirrors the crystal–melt interface structure

Despite over a century of studies, fundamental questions remain about the processes governing crystal nucleation from melts or solutions. Research over the past three decades has presented mounting evidence for kinetic pathways of crystal nucleation that are more complex than envisioned by the simplest forms of classical theory. Such observations have been presented for colloidal and elemental systems with covalent and metallic bonding. Despite the technological and geochemical importance of molten salts, similar studies for these ionically bonded systems are currently lacking. Here we develop a machine learning interatomic potential for a model ionic system: LiF. The potential features quantum-level accuracy for both liquid and multiple solid polymorphs over wide temperature and pressure ranges and accurately reproduces experimentally measured properties. Thanks to the efficiency of the potential, which enables microsecond-scale molecular dynamics simulations, induction times for nucleation of LiF solids from their melts are computed over a range of undercoolings. With the aid of a set of robust local order parameters established here, the simulations reveal that homogeneous crystal nucleation in undercooled melts preferentially initiates from liquid regions showing slow dynamics and high bond orientational order simultaneously, and the second-shell order of both precritical nuclei and the surface of postcritical nuclei is dominated by hexagonal close packing and body-centered cubic local structure, even though the nucleus core is dominated by face-centered cubic structure corresponding to the stable rocksalt crystal structure. Finally, we establish a connection between the crystallization pathway and the equilibrium crystal-melt interface structure.

Applied Physical Sciences↗
DOE OSTI2016

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels

Advances in quantitative mass spectrometry (MS)-based proteomics have sparked efforts to characterize the proteomes of tumor samples to provide complementary and unique information inaccessible by genomics. Tumor samples are usually not accrued with proteomic characterization in mind, raising concerns regarding effects of undocumented sample ischemia on protein abundance and phosphosite stoichiometry. Here we report the effects of cold ischemia time on clinical ovarian cancer samples and patient-derived basal and luminal breast cancer xenografts. Tumor tissues were excised and collected prior to vascular ligation, subjected to accurately defined ischemia times up to 60 min, and analyzed by quantitative proteomics and phosphoproteomics using isobaric tags and high-performance, multidimensional LC-MS/MS. No significant changes were detected at the protein level in each tumor type after 60 minutes of ischemia, and the majority of the >25,000 phosphosites detected were also stable. However, large, reproducible increases and decreases in protein phosphorylation at specific sites were observed in up to 24% of the phosphoproteome starting as early as 5 minutes post-excision. Early and sustained activation of stress response, transcriptional regulation and cell death pathways were observed in common across tumor types. Tissue-specific changes in phosphosite stability were also observed suggesting idiosyncratic effects of ischemia in particular lineages. Our study provides insights into the information that may be obtained by proteomic characterization of tumor samples after undocumented periods of ischemia, and suggests caution especially in interpreting activation of stress pathways in such samples as they may reflect sample handling rather than tumor physiology.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

Engineering transformation pathways in an Al 0.3 CoFeNi complex concentrated alloy leads to excellent strength–ductility combination

Guided by thermodynamic modeling, engineering phase transformation pathways via thermo-mechanical processing, in a complex concentrated alloy/high entropy alloy (HEA) of composition Al 0.3 CoFeNi, lead to a novel multi-scale microstructure consisting of fine-scale FCC + L1 2 grains mixed with B2 + BCC grains. The two-step pathway comprises initial decomposition of the parent single-phase FCC to form a fine-grained FCC + B2 microstructure, which further decomposes in the second step into the complex four-phase mixture, exhibiting an excellent combination of tensile yield stress of ~1490 MPa, ultimate tensile strength of ~1663 MPa, with a good ductility of ~12% at room temperature. This paper reports a novel multi-phase microstructure in a HEA/CCA similar to the microstructure observed in dual-phase stainless steel. This report exemplifies the novelty of HEA/CCA compositional space.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Pathways of bio-jet adoption in the US aviation industry with implications for the overall transportation and energy sectors: an integrated, multi-sectoral analysis of future scenarios

Bio-jet adoption has emerged as an attractive option to complement and supplement the use of refined fossil liquid fuels in the aviation industry in the US. However, there are significant uncertainties surrounding the costs of bio-jet including but not limited to costs of feedstock, transformation costs and the competition with co-products of bio-jet that may be demanded elsewhere in the transportation or energy sectors. This study models alternative trajectories of bio-jet adoption in the US aviation industry by 2050 through the use of a global integrated multi sector dynamics model. Three bio-jet production and consumption pathways are presented- soybean oil to jet, corn ethanol to jet (ETJ) and Fisher–Tropsch-based bio-jet, with each pathway explicitly considering the co-production of renewable diesel and renewable gasoline alongside the bio-jet. Without explicit actions or technology changes to offset the technology cost of bio-jet, scenarios where bio-jet displaces refined liquids result in higher aviation fuel prices (ranging from a 25% increase to 120% increase by mid-century) and lower demand (ranging from −14% to −43%). Corn ethanol will play an important role in the US if large scale amounts of bio-jet are to be produced with smaller effects on demand and prices. While scenarios with high levels of bio-jet availability without the availability of ETJ in the US can significantly reduce emissions in the aviation sector, these reductions are achieved more through the reduction in overall aviation fuel demand rather than technology adoption.

09 BIOMASS FUELS↗
DOE OSTI2025

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2020

Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis

Abstract Pennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.

13C-labeling↗
DOE OSTI2024

Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway

Abstract Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Metabolite fingerprinting of pennycress ( Thlaspi arvense L.) embryos to assess active pathways during oil synthesis

Pennycress ( Thlaspi arvense L.), a plant naturalized to North America, accumulates high levels of erucic acid in its seeds, which makes it a promising biodiesel and industrial crop. The main carbon sinks in pennycress embryos were found to be proteins, fatty acids, and cell wall, which respectively represented 38.5, 33.2, and 27.0% of the biomass at 21 days after pollination. Erucic acid reached a maximum of 36% of the total fatty acids. Together these results indicate that total oil and erucic acid contents could be increased to boost the economic competitiveness of this crop. Understanding the biochemical basis of oil synthesis in pennycress embryos is therefore timely and relevant to guide future breeding and/or metabolic engineering efforts. For this purpose, a combination of metabolomics approaches was conducted to assess the active biochemical pathways during oil synthesis. First, gas chromatography-mass spectrometry (GC-MS) profiling of intracellular metabolites highlighted three main families of compounds: organic acids, amino acids, and sugars/sugar alcohols. Secondly, these intermediates were quantified in developing pennycress embryos by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Finally, partitional clustering analysis grouped the intracellular metabolites that shared a similar pattern of accumulation over time into eight clusters. In conclusion, this study underlined that: (i) sucrose might be stored rather than cleaved into hexoses; (ii) glucose and glutamine would be the main sources of carbon and nitrogen, respectively; and (iii) glycolysis, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and the Calvin cycle were active in developing pennycress embryos.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Formation of S0s in extreme environments Ⅲ: the role of environment in the formation pathways

It is well established that there are at least two main channels to form lenticular (or S0) galaxies. The first, which we name ‘faded spiral’ scenario, includes quenching events that led to consumption or removal of gas from a spiral progenitor. The second, which we call ‘merger’ scenario, includes merger-like events and interactions between galaxies. Each scenario leaves characteristic signatures in the newly formed lenticular galaxy. However, the conditions that trigger one mechanism over another are still unknown. This paper is the third of a series aimed at understanding the role of the environment in the formation of lenticular galaxies. In this study, we combine the kinematics, morphology, and properties of the stellar populations of 329 S0s from the SAMI and MaNGA surveys in order to highlight the role of the environment in the process. We divide the S0s into two classes (A and B) according to their global properties, that we can associate to the products of a faded spiral scenario (class A) or a merger scenario (class B). Here we then study how the various classes are distributed within different environments. Our study reveals that the ‘faded spiral’ pathway is the most efficient channel to produce S0s, and it becomes more efficient as the mass of the group or cluster or local density of galaxies increase. The merger pathway is also a viable channel, and its efficiency becomes higher with decreasing local density or environment mass.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

A Novel Signaling Pathway Connects Thiamine Biosynthesis, Bacterial Respiration, and Production of the Exopolysaccharide Amylovoran in Erwinia amylovora

Erwinia amylovora is a plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. This bacterium colonizes host vascular tissues via the production of exopolysaccharides (EPSs) including amylovoran. It is well-established that the nearly ubiquitous plasmid pEA29 of E. amylovora is an essential virulence factor, but the underlying mechanism remains uncharacterized. Here, we demonstrated that pEA29 was required for E. amylovora to produce amylovoran and to form a biofilm, and this regulation was dependent on the thiamine biosynthesis operon thiOSGF. We then conducted carbohydrate and genetic analyses demonstrating that the thiamine-mediated effect on amylovoran production was indirect, as cells lacking thiOSGF produced an EPS that did not contain glucuronic acid, one of the key components of amylovoran, whereas the transcriptional activity and RNA levels of the amylovoran biosynthesis genes were not altered. Alternatively, addition of exogenous thiamine restored amylovoran production in the pEA29-cured strain of E. amylovora and positively impacted amylovoran production in a dose-dependent manner. Individual deletion of several chromosomal thiamine biosynthesis genes also affected amylovoran production, implying that a complete thiamine biosynthesis pathway is required for the thiamine-mediated effect on amylovoran production in E. amylovora. Finally, we determined that an imbalanced tricarboxylic acid cycle negatively affected amylovoran production, which was restored by addition of exogenous thiamine or overexpression of the thiOSGF operon. In summary, our report revealed a novel signaling pathway that impacts E. amylovora virulence in which thiamine biosynthesis enhances bacterial respiration that provides energetic requirements for the biosynthesis of EPS amylovoran.

59 BASIC BIOLOGICAL SCIENCES↗