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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 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

In Situ Atmospheric Plume Thermometry via Carbon Monoxide Spectral Profile: Laboratory and Field Validation

For small molecules with large rotational constants, knowing the relative intensities of the ro-vibrational transitions can be used to determine the temperature within a gas plume. We demonstrate the use of carbon monoxide (CO) as an in situ spectroscopic probe of gas plume temperature by application of both laboratory and standoff Fourier transform infrared spectroscopy to monitor the CO spectral response at different temperatures. Here, the measured CO rotational contours were analyzed using a simple Boltzmann model to deduce the population distribution of the J-levels, from which the in-plume temperature is deduced. The method was vetted by comparing deduced temperatures in both static laboratory measurements of known temperatures, as well as field measurements using a simulated smokestack release. For the smokestack experiments, spectroscopically deduced temperatures were compared to readings from a series of thermocouples placed at strategically sampled distances along the plume trajectory. Both the spectroscopically-derived and thermocouple-measured temperatures revealed an expansion-induced (mixing) rapid cooling of the plume, with the infrared thermometry values displaying greater temperature values which are believed to better represent the actual plume temperatures.

Analysis of rotational structure↗
DOE OSTI2018

Operation Mechanism of Perovskite Quantum Dot Solar Cells Probed by Impedance Spectroscopy

We fabricated perovskite quantum dot solar cells (PQDSCs) and varied the thickness of the QD layer by controlling the number of deposition cycles; the cells were systematically investigated with impedance spectroscopy. Despite the evident structural differences with respect to standard perovskite solar cells (PSCs), similar impedance spectra were obtained for PQDSCs, pointing to similar working principles in terms of the active layer. We distinguish two different regimes: At low illumination, recombination is ruled by multiple trapping with trap distributions and/or shunting. However, at higher light intensities, Shockley-Read-Hall recombination is observed. In addition, the low-frequency capacitance, CLF, of PQDSCs increases several orders of magnitude when the illumination is varied from dark to 1-sun conditions. This feature has not been observed in other kinds of photovoltaic devices and is characteristic of PSCs. Although there is no consensus about the exact mechanism responsible for CLF, the suggested models point to an ion migration origin. Its observation in thin-film and PQDSCs devices implies a similar effect in both.

14 SOLAR ENERGY↗
DOE OSTI2026

Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra

Identifying molecular structure based on spectroscopic readings is a key task in a variety of chemical and biological applications. Common spectroscopy techniques, such as Infrared (IR) Spectroscopy and Mass Spectrometry (MS), provide detailed information on the structure of molecular compounds but nonetheless require expert-level knowledge to decode. Machine learning has emerged as a potential solution for automating structure prediction from chemical spectra; however, current approaches generally focus on single sensor modalities, neglecting to leverage the complementary information contained within differing spectra. In this paper, we introduce Peak2Patch, a novel approach to fusion-enhanced prediction of functional groups from IR and mass spectra. First, we perform a detailed comparison of backbone networks for encoding both sparse mass spectra and dense IR spectra and demonstrate the superior performance of transformer neural networks over current state-of-the-art convolutional neural networks. Second, we evaluate three broad categories of fusion: early (raw feature), middle (deep feature), and late (decision) fusion, demonstrating the potential of a deep feature fusion-based approach. Lastly, we present Peak2Patch, our attention-based fusion scheme, which leverages cross-attention to mix features between encoded tokens of the two modalities. We validate our approach on a publicly available multimodal spectroscopic data set of 790k simulated molecules, demonstrating a large improvement in functional group prediction over both the previous state-of-the-art and our own strong single-modal baselines.

Jacobson, Philip [Sandia National Laboratories (SN↗
DOE OSTI2015

Onset of the Efficiency Droop in GaInN Quantum Well Light-Emitting Diodes under Photoluminescence and Electroluminescence Excitation

The efficiency of Ga0.87In0.13N/GaN single and multiple quantum well (QW) light-emitting diodes is investigated under photoluminescence (PL) and electroluminescence (EL) excitation. By measuring the laser spot area (knife-edge method) and the absorbance of the GaInN QW (transmittance/reflectance measurements), the PL excitation density can be converted to an equivalent EL excitation density. The EL efficiency droop-onset occurs at an excitation density of 2.08 × 1026 cm–3 s–1 (J = 10 A/cm2), whereas no PL efficiency droop is found for excitation densities as high as 3.11 × 1027 cm–3 s–1 (J = 149 A/cm2). Considering Shockley–Read–Hall, radiative, and Auger recombination and including carrier leakage shows that the EL efficiency droop is consistent with a reduction of injection efficiency.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae

The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this intricate puzzle. Here, we applied a previously developed auxin-inducible depletion of hexokinase 2 as a metabolic engineering strategy for improved nerolidol production in Saccharomyces cerevisiae, and biological replicates exhibit a dichotomy in nerolidol production of either 3.5 or 2.5 g L –1 nerolidol. Harnessing Oxford Nanopore’s long-read genomic sequencing, we reveal a potential genetic cause—the chromosome integration of a 2μ sequence-based yeast episomal plasmid, encoding the expression cassettes for nerolidol synthetic enzymes. This finding was reinforced through chromosome integration revalidation, engineering nerolidol and valencene production strains, and generating a diverse pool of yeast clones, each uniquely fingerprinted by gene copy numbers, plasmid integrations, other genomic rearrangements, protein expression levels, growth rate, and target product productivities. Τhe best clone in two strains produced 3.5 g L –1 nerolidol and ~0.96 g L –1 valencene. Comparable genotypic and phenotypic variations were also generated through the integration of a yeast integrative plasmid lacking 2μ sequences. Our work shows that multiple factors, including plasmid integration status, subchromosomal location, gene copy number, sesquiterpene synthase expression level, and genome rearrangement, together play a complicated determinant role on the productivities of sesquiterpene product. Integration of yeast episomal/integrative plasmids may be used as a versatile method for increasing the diversity and optimizing the efficiency of yeast cell factories, thereby uncovering metabolic control mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Using Methyl Bromide for Interspecies Cell–Cell Signaling and As a Reporter in a Model Soil Consortium

Synthetic microbial communities are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five member MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that Variovorax beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally-relevant hydration conditions. We find that methyl halide production can report on a MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. Finally, these tools will be useful for future studies that investigate how MSC respond to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Genetic Toolbox for Modulating the Expression of Heterologous Genes in the Cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide, and in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp. PCC 6803. We report the finding that the E. coli σ 70 promoter Ptrc is superior compared to the previously reported strong promoters, such as PcpcB and PpsbA, for the expression of EFE. In addition, we found that the EFE expression level was very sensitive to the 5'-untranslated region upstream of the open reading frame. A library of ribosome binding sites (RBSs) was rationally designed and was built and systematically characterized. We demonstrate a strategy complementary to the RBS prediction software to facilitate the rational design of an RBS library to optimize the gene expression in cyanobacteria. Our results show that the EFE expression level is dramatically enhanced through these synthetic biology tools and is no longer the rate-limiting step for cyanobacterial ethylene production. Furthermore, these systematically characterized promoters and the RBS design strategy can serve as useful tools to tune gene expression levels and to identify and mitigate metabolic bottlenecks in cyanobacteria.

09 BIOMASS FUELS↗
DOE OSTI2013

Carbon/Ternary Alloy/Carbon Optical Stack on Mylar as an Optical Data Storage Medium to Potentially Replace Magnetic Tape

A novel write-once-read-many (WORM) optical stack on Mylar tape is proposed as a replacement for magnetic tape for archival data storage. This optical tape contains a cosputtered bismuth–tellurium–selenium (BTS) alloy as the write layer sandwiched between thin, protective films of reactively sputtered carbon. The composition and thickness of the BTS layer were confirmed by Rutherford Backscattering (RBS) and atomic force microscopy (AFM), respectively. The C/BTS/C stack on Mylar was written to/marked by 532 nm laser pulses. Under the same conditions, control Mylar films without the optical stack were unaffected. Marks, which showed craters/movement of the write material, were characterized by optical microscopy and AFM. The threshold laser powers for making marks on C/BTS/C stacks with different thicknesses were explored. Higher quality marks were made with a 60× objective compared to a 40× objective in our marking apparatus. Finally, the laser writing process was simulated with COMSOL.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Formation mechanism of the secondary building unit in a chromium terephthalate metal-organic framework

Based on density functional theory calculations and simulation, a detailed mechanism is presented on the formation of the secondary building unit (SBU) of MIL-101, a chromium terephthalate metal-organic framework (MOF). SBU formation is key to MOF nucleation, the rate-limiting step in the formation process of many MOFs. A series of reactions that lead to the formation of the SBU of MIL-101 is proposed in this work. Initial rate-limiting reactions form the metal cluster with three chromium (III) atoms linked to a central bridging oxygen. Terephthalate linkers play a key role as chromium (III) atoms are joined to linker carboxylate groups prior to the placement of the central bridging oxygen. Multiple linker addition reactions, which follow in different paths due to structural isomers, are limited by the removal of water molecules in the first chromium coordination shell. The least energy path is identified were all linkers on one face of the metal center plane are added first. A simple kinetic model based on transition state theory shows the rate of secondary building unit formation similar to the rate metal-organic framework nucleation. The authors are thankful to Dr. R. Rousseau for a critical reading of the manuscript. This research would not have been possible without the support of the Office of Fossil Energy, U.S. Department of Energy. This research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and the PNNL Institutional Computing (PIC) program located at Pacific Northwest National Laboratory.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Discovery of protein- and DNA-imperceptible nanoparticle hard coating using gel-based reaction tuning

The seemingly inevitable protein corona appears to be an insurmountable obstacle to wider application of functional nanomaterials in biotechnology. The accumulation of serum proteins can block targeting functionalities and alter the in vivo fate of these nanomaterials. Here we demonstrate a method to generate non-stick, robustly passivated functional nanoparticles (NPs) using a tailored silica coating. We apply agarose gel electrophoresis to sensitively evaluate protein binding to NPs with different surface chemistry. Using gel banding and retardation as a read-out for protein adsorption, we optimize the surface chemistry to yield a mixed charge surface which displays remarkable binding resistance to a wide range of serum proteins and nucleic acids. Here, the hard silica shell also protects the functional NP core in harsh environments (down to pH 1) while still showing the ability to be targeted for cellular uptake with little or no non-specific binding.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Trigonal Bipyramidal V 3+ Complex as an Optically Addressable Molecular Qubit Candidate

Synthetic chemistry enables a bottom-up approach to quantum information science, where atoms can be deterministically positioned in a quantum bit or qubit. Two key requirements to realize quantum technologies are qubit initialization and read-out. By imbuing molecular spins with optical initialization and readout mechanisms, analogous to solid-state defects, molecules could be integrated into existing quantum infrastructure. To mimic the electronic structure of optically addressable defect sites, we designed the spin-triplet, V 3+ complex, (C 6 F 5 ) 3 trenVCN t Bu (1).We measured the static spin properties as well as the spin coherence time of1demonstrating coherent control of this spin qubit with a 240 GHz electron paramagnetic resonance spectrometer powered by a free electron laser. We found that1exhibited narrow, near-infrared photoluminescence (PL) from a spin-singlet excited state. Using variable magnetic field PL spectroscopy, we resolved emission into each of the ground-state spin sublevels, a crucial component for spin-selective optical initialization and readout. This work demonstrates that trigonally symmetric, heteroleptic V 3+ complexes are candidates for optical spin addressability.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2025

Coherent Control over Nuclear Hyperpolarization Using an Optically Initializable Chromophore-Radical System

Chromophore radicals (CR) are emerging as important components for molecular quantum information science (QIS), especially in the context of quantum sensing. Here, we demonstrate that the optically hyperpolarized electrons in a 1,6,7,12-tetrakis(4-tert-butylphenoxy)-perylene-3,4,9,10-bis(dicarboximide) (tpPDI) covalently linked to a partially deuterated 1,3-bis(diphenylene)-d 16 -2-phenylallyl radical (BDPA-d 16 ) can be coherently manipulated via pulsed dynamic nuclear polarization (DNP) methods to transfer polarization to nuclear spins and back. Under light illumination at 85 K, electron hyperpolarization in BDPA is enhanced 2.1- to 2.4-fold over thermal polarization and lasts for more than 100 ms. By applying nuclear orientation via electron spin-locking (NOVEL) DNP, this optically amplified electron hyperpolarization was successfully transferred to a 1 H nuclear spin within the CR system and efficiently returned to the electron spin for readout via reverse-NOVEL. The NOVEL transfer efficiency of 65% amounts to a 688-fold nuclear spin hyperpolarization of the target nuclear spin, considering the 2.1-fold electron spin hyperpolarization. This reversible coherent manipulation of hyperpolarization transfer highlights the utility of CR systems to initialize and read out nuclear spin states in a disordered matrix at moderate cryogenic temperatures. Coupled with CRs’ environmental compatibility, tunability, and precise state initialization, these results highlight the promising role of nuclear spins in CRs for QIS applications, including quantum sensing and memory.

charge transfer↗
DOE OSTI2019

Thank You to Our 2018 Peer Reviewers

On behalf of the journal, AGU, and the scientific community, the Editors would like to sincerely thank those who reviewed manuscripts for Geophysical Research Letters in 2018. The hours reading and commenting on manuscripts not only improves the manuscripts but also increases the scientific rigor of future research in the field. We particularly appreciate the timely reviews, in light of the demands imposed by the rapid review process at Geophysical Research Letters. With the revival of the “major revisions” decisions, we appreciate the reviewers' efforts on multiple versions of some manuscripts. Many of those listed below went beyond and reviewed three or more manuscripts for our journal, and those are indicated in italics. In total, 4,484 referees contributed to 7,557 individual reviews in journal. Thank you again. We look forward to the coming year of exciting advances in the field and communicating those advances to our community and to the broader public.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2014

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ~ 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. Here, we conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. Furthermore, a combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. This study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.

58 GEOSCIENCES↗
DOE OSTI2016

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A stable transcription factor complex nucleated by oligomeric AML1–ETO controls leukaemogenesis

Transcription factors are frequently altered in leukaemia through chromosomal translocation, mutation or aberrant expression. AML1–ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukaemia, is a transcription factor implicated in both gene repression and activation. AML1–ETO oligomerization, mediated by the NHR2 domain, is critical for leukaemogenesis, making it important to identify co-regulatory factors that ‘read’ the NHR2 oligomerization and contribute to leukaemogenesis. Here we show that, in human leukaemic cells, AML1–ETO resides in and functions through a stable AML1–ETO-containing transcription factor complex (AETFC) that contains several haematopoietic transcription (co)factors. These AETFC components stabilize the complex through multivalent interactions, provide multiple DNA-binding domains for diverse target genes, co-localize genome wide, cooperatively regulate gene expression, and contribute to leukaemogenesis. Within the AETFC complex, AML1–ETO oligomerization is required for a specific interaction between the oligomerized NHR2 domain and a novel NHR2-binding (N2B) motif in E proteins. Crystallographic analysis of the NHR2–N2B complex reveals a unique interaction pattern in which an N2B peptide makes direct contact with side chains of two NHR2 domains as a dimer, providing a novel model of how dimeric/oligomeric transcription factors create a new protein-binding interface through dimerization/oligomerization. Intriguingly, disruption of this interaction by point mutations abrogates AML1–ETO-induced haematopoietic stem/progenitor cell self-renewal and leukaemogenesis. These results reveal new mechanisms of action of AML1–ETO, and provide a potential therapeutic target in t(8;21)-positive acute myeloid leukaemia.

Sun, Xiao-Jian↗