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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The diversity of three-dimensional photonic crystals

Many butterflies, birds, beetles, and chameleons owe their spectacular colors to the microscopic patterns within their wings, feathers, or skin. When these patterns, or photonic crystals, result in the omnidirectional reflection of commensurate wavelengths of light, it is due to a complete photonic band gap (PBG). The number of natural crystal structures known to have a PBG is relatively small, and those within the even smaller subset of notoriety, including diamond and inverse opal, have proven difficult to synthesize. Here, we report more than 150,000 photonic band calculations for thousands of natural crystal templates from which we predict 351 photonic crystal templates – including nearly 300 previously-unreported structures – that can potentially be realized for a multitude of applications and length scales, including several in the visible range via colloidal self-assembly. With this large variety of 3D photonic crystals, we also revisit and discuss oft-used primary design heuristics for PBG materials.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens

Chimeric antigen receptor (CAR) T cells have emerged as a promising class of therapeutic agents, generating remarkable responses in the clinic for a subset of human cancers. One major challenge precluding the wider implementation of CAR therapy is the paucity of tumor-specific antigens. Here, we describe the development of a CAR targeting the tumor-specific isocitrate dehydrogenase 2 (IDH2) with R140Q mutation presented on the cell surface in complex with a common human leukocyte antigen allele, HLA-B*07:02. Engineering of the hinge domain of the CAR, as well as crystal structure-guided optimization of the IDH2 R140Q- HLA-B*07:02-targeting moiety, enhances the sensitivity and specificity of CARs to enable targeting of this HLA-restricted neoantigen. This approach thus holds promise for the development and optimization of immunotherapies specific to other cancer driver mutations that are difficult to target by conventional means.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Abstract Lung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value.

Beyett, Tyler S. (ORCID:0000000155097004)↗
DOE OSTI2023

Next-generation large-scale binary protein interaction network for Drosophila melanogaster

Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Nonlinear multi-magnon scattering in artificial spin ice

Abstract Magnons, the quantum-mechanical fundamental excitations of magnetic solids, are bosons whose number does not need to be conserved in scattering processes. Microwave-induced parametric magnon processes, often called Suhl instabilities, have been believed to occur in magnetic thin films only, where quasi-continuous magnon bands exist. Here, we reveal the existence of such nonlinear magnon-magnon scattering processes and their coherence in ensembles of magnetic nanostructures known as artificial spin ice. We find that these systems exhibit effective scattering processes akin to those observed in continuous magnetic thin films. We utilize a combined microwave and microfocused Brillouin light scattering measurement approach to investigate the evolution of their modes. Scattering events occur between resonance frequencies that are determined by each nanomagnet’s mode volume and profile. Comparison with numerical simulations reveals that frequency doubling is enabled by exciting a subset of nanomagnets that, in turn, act as nanosized antennas, an effect that is akin to scattering in continuous films. Moreover, our results suggest that tunable directional scattering is possible in these structures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

The evolution of dam induced river fragmentation in the United States

It is established that dams decrease river connectivity; however, previous global scale studies of river fragmentation focused on a small subset of the largest dams. In the United States, mid-sized dams, which are too small for global databases, account for 96% of major anthropogenic structures and 48% of reservoir storage. We conduct a national evaluation of the evolution of anthropogenic river bifurcation over time that includes more than 50,000 nationally inventoried dams. Mid-sized dams account for 73% of anthropogenically created stream fragments nationally. They also contribute disproportionately to short fragments (less than 10 km), which is particularly troubling for aquatic habitats. Here we show that dam construction has essentially reversed natural fragmentation patterns in the United States. Prior to human development, smaller river fragments and less connected networks occurred in arid basins while today we show that humid basins are the most fragmented due to human structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Demonstration of an AI-driven workflow for autonomous high-resolution scanning microscopy

Abstract Modern scanning microscopes can image materials with up to sub-atomic spatial and sub-picosecond time resolutions, but these capabilities come with large volumes of data, which can be difficult to store and analyze. We report the Fast Autonomous Scanning Toolkit (FAST) that addresses this challenge by combining a neural network, route optimization, and efficient hardware controls to enable a self-driving experiment that actively identifies and measures a sparse but representative data subset in lieu of the full dataset. FAST requires no prior information about the sample, is computationally efficient, and uses generic hardware controls with minimal experiment-specific wrapping. We test FAST in simulations and a dark-field X-ray microscopy experiment of a WSe 2 film. Our studies show that a FAST scan of <25% is sufficient to accurately image and analyze the sample. FAST is easy to adapt for any scanning microscope; its broad adoption will empower general multi-level studies of materials evolution with respect to time, temperature, or other parameters.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms

Abstract Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax , supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural insights into opposing actions of neurosteroids on GABA A receptors

γ-Aminobutyric acid type A (GABA A ) receptors mediate fast inhibitory signaling in the brain and are targets of numerous drugs and endogenous neurosteroids. A subset of neurosteroids are GABA A receptor positive allosteric modulators; one of these, allopregnanolone, is the only drug approved specifically for treating postpartum depression. There is a consensus emerging from structural, physiological and photolabeling studies as to where positive modulators bind, but how they potentiate GABA activation remains unclear. Other neurosteroids are negative modulators of GABA A receptors, but their binding sites remain debated. Here we present structures of a synaptic GABA A receptor bound to allopregnanolone and two inhibitory sulfated neurosteroids. Allopregnanolone binds at the receptor-bilayer interface, in the consensus potentiator site. In contrast, inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support a mechanism by which allopregnanolone potentiates channel activity and suggest the dominant mechanism for sulfated neurosteroid inhibition is through pore block.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for autoinhibition by the dephosphorylated regulatory domain of Ycf1

Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Neuromorphic overparameterisation and few-shot learning in multilayer physical neural networks

Abstract Physical neuromorphic computing, exploiting the complex dynamics of physical systems, has seen rapid advancements in sophistication and performance. Physical reservoir computing, a subset of neuromorphic computing, faces limitations due to its reliance on single systems. This constrains output dimensionality and dynamic range, limiting performance to a narrow range of tasks. Here, we engineer a suite of nanomagnetic array physical reservoirs and interconnect them in parallel and series to create a multilayer neural network architecture. The output of one reservoir is recorded, scaled and virtually fed as input to the next reservoir. This networked approach increases output dimensionality, internal dynamics and computational performance. We demonstrate that a physical neuromorphic system can achieve an overparameterised state, facilitating meta-learning on small training sets and yielding strong performance across a wide range of tasks. Our approach’s efficacy is further demonstrated through few-shot learning, where the system rapidly adapts to new tasks.

Science & Technology - Other Topics↗
DOE OSTI2025

Pd/C promotes C–H bond activation and oxidation of p -hydroxybenzoate during hydrogenolysis of poplar

Hydrogenolysis of lignin generates a portfolio of products, the yields of which are generally calculated using a subset of phenolic monomers that are dependent on the lignin composition, product distribution, and analytical technique. Some lignins are naturally γ-acylated; poplar lignins, for example, have p-hydroxybenzoate groups on 1–15% of their syringyl subunits. Upon hydrogenolysis, it is generally assumed that the p-hydroxybenzoate is cleaved before the deacylated lignin is depolymerized. Hydrogenolysis of model γ-p-hydroxybenzoylated β-aryl ethers do not, however, produce the deacylated β-aryl ether intermediates, as was previously conjectured; products instead derive from palladium-assisted reactions on the cinnamyl p-hydroxybenzoates resulting in initial β-ether cleavage. The p-hydroxybenzoate moiety itself also undergoes carboxylate-assisted palladium-catalyzed C–H bond activation to form the 2,4-dihydroxybenzoate, that subsequently converts to the 2,4-dihydroxycyclohex-1-enoate. Furthermore, these details underscore previously unrecognized pathways and products that are key to understanding the different hydrogenolysis product distributions from naturally acylated lignins that are prevalent biomass-conversion feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2025

Efficient up-conversion in CsPbBr 3 nanocrystals via phonon-driven exciton-polaron formation

Lead halide perovskite nanocrystals demonstrate efficient up-conversion, although the precise mechanism remains a subject of active research. This study utilizes steady-state and time-resolved spectroscopy methods to unravel the mechanism driving the up-conversion process in CsPbBr 3 nanocrystals. Employing above- and below-gap photoluminescence measurements, we extract a distinct phonon mode with an energy of ~7 meV and identify the Pb-Br-Pb bending mode as the phonon involved in the up-conversion process. This result was corroborated by Raman spectroscopy. We confirm an up-conversion efficiency reaching up to 75%. Transient absorption measurements under conditions of sub-gap excitation also unexpectedly reveal coherent phonons for the subset of nanocrystals undergoing up-conversion. This coherence implies that the up-conversion and subsequent relaxation is accompanied by a synchronized and phased lattice motion. This study reveals that efficient up-conversion in CsPbBr 3 nanocrystals is powered by a unique interplay between the soft lattice structure, phonons, and excited states dynamics.

Anti-Stokes Photoluminescence↗
DOE OSTI2025

Identification of functional non-coding variants associated with orofacial cleft

Oral facial cleft (OFC) comprises cleft lip with or without cleft palate (CL/P) or cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) in many genomic loci where the presumed effector gene (for example, IRF6 in the 1q32 locus) is expressed in embryonic oral epithelium. To identify candidates for functional SNPs at eight such loci we conduct a massively parallel reporter assay in a fetal oral epithelial cell line, revealing SNPs with allele-specific effects on enhancer activity. We filter these SNPs against chromatin-mark evidence of enhancers and test a subset in traditional reporter assays, which support the candidacy of SNPs at loci containing FOXE1, IRF6, MAFB, TFAP2A, and TP63. For two SNPs near IRF6 and one near FOXE1, we engineer the genome of induced pluripotent stem cells, differentiate the cells into embryonic oral epithelium, and discover allele-specific effects on the levels of effector gene expression, and, in two cases, the binding affinity of transcription factors FOXE1 or ETS2. Conditional analyses of GWAS data suggest the two functional SNPs near IRF6 account for the majority of risk for CL/P at this locus. This study connects genetic variation associated with OFC to mechanisms of pathogenesis.

Kumari, Priyanka↗
DOE OSTI2026

Duration of super-emitting oil and gas methane sources

The duration of super-emitting events (>100 kg h -1 ) in oil and gas basins remains insufficiently understood but is key for reporting programs and mitigation strategies. Carbon Mapper conducted aerial surveys from April 30 to May 17, 2024, over the New Mexico Permian Basin, covering 276,000 wells, 1100 compressor stations, 175 gas processing plants, and 27,000 km of pipeline. We find over 500 super-emitting sources with 300 of these sources observed repeatedly across multiple days. We quantify total super emissions by integrating individual events with observationally constrained event durations (5.98 −14.7 Gg CH 4 ) and compare to total emissions derived from basin average snapshots (12.7 ± 0.92 Gg CH 4 ). This gap between emission estimates is reconciled through assumptions on missed detections, characteristic event duration, detection frequency, and diurnal variability. Emission events generally lasted for at least 2 hours, and a small subset of sources (18 total), persistently emitted throughout the entire campaign, representing a near-term opportunity for mitigation. When compared to regional flux estimates derived from independent observations, we estimate super-emitters to contribute approximately 50% (37-73%) towards total emissions. Frequent wide-area monitoring is crucial for capturing rare super-emitter events that, together with other emission sources, drive basin-level variability and emission intensity.

Cusworth, Daniel H. [Carbon Mapper, Pasadena, CA (↗
DOE OSTI2024

Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

Abstract The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant–fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.

59 BASIC BIOLOGICAL SCIENCES↗