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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Point-by-point inscribed sapphire parallel fiber Bragg gratings in a fully multimode system for multiplexed high-temperature sensing

In this work, we study the point-by-point inscription of sapphire parallel fiber Bragg gratings (sapphire pFBGs) in a fully multimode system. A parallel FBG is shown to be critical in enabling detectable and reliable high-order grating signals. The impacts of modal volume, spatial coherence, and grating location on reflectivity are examined. Three cascaded seventh-order pFBGs are fabricated in one sapphire fiber for wavelength multiplexed temperature sensing. Using a low-cost, fully multimode 850-nm interrogator, reliable measurement up to 1500°C is demonstrated.

42 ENGINEERING↗
DOE OSTI2023

Integrated photonic molecule Brillouin laser with a high-power sub-100-mHz fundamental linewidth

Photonic integrated lasers with an ultra-low fundamental linewidth and a high output power are important for precision atomic and quantum applications, high-capacity communications, and fiber sensing, yet wafer-scale solutions have remained elusive. Here we report an integrated stimulated Brillouin laser (SBL), based on a photonic molecule coupled resonator design, that achieves a sub-100-mHz fundamental linewidth with greater than 10-mW output power in the C band, fabricated on a 200-mm silicon nitride (Si 3 N 4 ) CMOS-foundry compatible wafer-scale platform. The photonic molecule design is used to suppress the second-order Stokes (S2) emission, allowing the primary lasing mode to increase with the pump power without phase noise feedback from higher Stokes orders. The nested waveguide resonators have a 184 million intrinsic and 92 million loaded Q, over an order of magnitude improvement over prior photonic molecules, enabling precision resonance splitting of 198 MHz at the S2 frequency. We demonstrate S2-suppressed single-mode SBL with a minimum fundamental linewidth of 71±18 mHz, corresponding to a 23±6-mHz 2 /Hz white-frequency-noise floor, over an order of magnitude lower than prior integrated SBLs, with an ∼11-mW output power and 2.3-mW threshold power. The frequency noise reaches the resonator-intrinsic thermo-refractive noise from 2-kHz to 1-MHz offset. The laser phase noise reaches −155 dBc/Hz at 10-MHz offset. The performance of this chip-scale SBL shows promise not only to improve the reliability and reduce size and cost but also to enable new precision experiments that require the high-speed manipulation, control, and interrogation of atoms and qubits. Realization in the silicon nitride ultra-low loss platform is adaptable to a wide range of wavelengths from the visible to infrared and enables integration with other components for systems-on-chip solutions for a wide range of precision scientific and engineering applications including quantum sensing, gravitometers, atom interferometers, precision metrology, optical atomic clocks, and ultra-low noise microwave generation.

Liu, Kaikai (ORCID:0000000213609646)↗
DOE OSTI2021

Integrated reference cavity with dual-mode optical thermometry for frequency correction

Photonic integrated resonators have advantages over traditional benchtop cavities in terms of size, weight, and cost with the potential to enable applications that require spectrally pure light. However, integrated resonators suffer from temperature-dependent frequency variations and are sensitive to external environmental perturbations, which hinders their usage in precision frequency applications. One solution is to use interrogation of the cavity temperature through dual-mode optical thermometry (DMOT) by measuring the shift of the resonance frequency difference between two polarization or optical frequency modes. Yet this approach has only been demonstrated in bulk-optic whispering gallery mode and fiber resonators. In this paper, we implement dual-mode optical thermometry in an ultra-high Q integrated silicon nitride resonator. A dual-mode resonance frequency difference temperature sensitivity of 188 ± <#comment/> 15 M H z / K is measured. We demonstrate feedforward DMOT frequency correction that, under an applied external temperature ramp, is able to reduce the optical frequency change to 0.31 kHz/s as compared to an uncorrected 10.03 kHz/s, a factor of 30 × <#comment/> reduction. These results show promise for on-chip frequency correction solutions for quantum, metrology, atomic, and coherent optical communications applications.

Zhao, Qiancheng (ORCID:0000000206968667)↗
DOE OSTI2024

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Computational and empirical studies predict Mycobacterium tuberculosis -specific T cells as a biomarker for infection outcome

Identifying biomarkers for tuberculosis (TB) is an ongoing challenge in developing immunological correlates of infection outcome and protection. Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines. To effectively predict biomarkers for infection progression in any disease, including TB, large amounts of experimental data are required to reach statistical power and make accurate predictions. We took a two-pronged approach using both experimental and computational modeling to address this problem. We first collected 200 blood samples over a 2-year period from 28 non-human primates (NHP) infected with a low dose of Mycobacterium tuberculosis . We identified T cells and the cytokines that they were producing (single and multiple) from each sample along with monkey status and infection progression data. Machine learning techniques were used to interrogate the experimental NHP datasets without identifying any potential TB biomarker. In parallel, we used our extensive novel NHP datasets to build and calibrate a multi-organ computational model that combines what is occurring at the site of infection (e.g., lung) at a single granuloma scale with blood level readouts that can be tracked in monkeys and humans. We then generated a large in silico repository of in silico granulomas coupled to lymph node and blood dynamics and developed an in silico tool to scale granuloma level results to a full host scale to identify what best predicts Mycobacterium tuberculosis (Mtb) infection outcomes. The analysis of in silico blood measures identifies Mtb -specific frequencies of effector T cell phenotypes at various time points post infection as promising indicators of infection outcome. As a result, we emphasize that pairing wetlab and computational approaches holds great promise to accelerate TB biomarker discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels

Generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. One of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic hydrolysis. Biomass pretreatment with ionic liquids (ILs) enables efficient saccharification of biomass, but residual ILs inhibit both saccharification and microbial fuel production, requiring extensive washing after IL pretreatment. Pretreatment itself can also produce biomass-derived inhibitory compounds that reduce microbial fuel production. Therefore, there are multiple points in the process from biomass to biofuel production that must be interrogated and optimized to maximize fuel production. Here, we report the development of an IL-tolerant cellulase cocktail by combining thermophilic bacterial glycoside hydrolases produced by a mixed consortia with recombinant glycoside hydrolases. This enzymatic cocktail saccharifies IL-pretreated biomass at higher temperatures and in the presence of much higher IL concentrations than commercial fungal cocktails. Sugars obtained from saccharification of IL-pretreated switchgrass using this cocktail can be converted into biodiesel (fatty acid ethyl-esters or FAEEs) by a metabolically engineered strain of E. coli . During these studies, we found that this biodiesel-producing E. coli strain was sensitive to ILs and inhibitors released by saccharification. This cocktail will enable the development of novel biomass to biofuel bioprocessing configurations that may overcome some of the barriers to production of inexpensive cellulosic biofuels.

09 BIOMASS FUELS↗
DOE OSTI2012

Inference of Causal Networks from Time-Varying Transcriptome Data via Sparse Coding

Temporal analysis of genome-wide data can provide insights into the underlying mechanism of the biological processes in two ways. First, grouping the temporal data provides a richer, more robust representation of the underlying processes that are co-regulated. The net result is a significant dimensional reduction of the genome-wide array data into a smaller set of vocabularies for bioinformatics analysis. Second, the computed set of time-course vocabularies can be interrogated for a potential causal network that can shed light on the underlying interactions. The method is coupled with an experiment for investigating responses to high doses of ionizing radiation with and without a small priming dose. From a computational perspective, inference of a causal network can rapidly become computationally intractable with the increasing number of variables. Additionally, from a bioinformatics perspective, larger networks always hinder interpretation. Therefore, our method focuses on inferring the simplest network that is computationally tractable and interpretable. The method first reduces the number of temporal variables through consensus clustering to reveal a small set of temporal templates. It then enforces simplicity in the network configuration through the sparsity constraint, which is further regularized by requiring continuity between consecutive time points. We present intermediate results for each computational step, and apply our method to a time-course transcriptome dataset for a cell line receiving a challenge dose of ionizing radiation with and without a prior priming dose. Our analyses indicate that (i) the priming dose increases the diversity of the computed templates (e.g., diversity of transcriptome signatures); thus, increasing the network complexity; (ii) as a result of the priming dose, there are a number of unique templates with delayed and oscillatory profiles; and (iii) radiation-induced stress responses are enriched through pathway and subnetwork studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses

Respiratory infections stemming from influenza viruses and the Severe Acute Respiratory Syndrome corona virus (SARS-CoV) represent a serious public health threat as emerging pandemics. Despite efforts to identify the critical interactions of these viruses with host machinery, the key regulatory events that lead to disease pathology remain poorly targeted with therapeutics. Here we implement an integrated network interrogation approach, in which proteome and transcriptome datasets from infection of both viruses in human lung epithelial cells are utilized to predict regulatory genes involved in the host response. We take advantage of a novel “crowd-based” approach to identify and combine ranking metrics that isolate genes/proteins likely related to the pathogenicity of SARS-CoV and influenza virus. Subsequently, a multivariate regression model is used to compare predicted lung epithelial regulatory influences with data derived from other respiratory virus infection models. We predicted a small set of regulatory factors with conserved behavior for consideration as important components of viral pathogenesis that might also serve as therapeutic targets for intervention. Our results demonstrate the utility of integrating diverse ‘omic datasets to predict and prioritize regulatory features conserved across multiple pathogen infection models.

Computational Biology↗
DOE OSTI2014

Expression of a Humanized Viral 2A-Mediated lux Operon Efficiently Generates Autonomous Bioluminescence in Human Cells

Expression of autonomous bioluminescence from human cells was previously reported to be impossible, suggesting that all bioluminescent-based mammalian reporter systems must therefore require application of a potentially influential chemical substrate. While this was disproven when the bacterial luciferase (lux) cassette was demonstrated to function in a human cell, its expression required multiple genetic constructs, was functional in only a single cell type, and generated a significantly reduced signal compared to substrate-requiring systems. Here we investigate the use of a humanized, viral 2A-linked lux genetic architecture for the efficient introduction of an autobioluminescent phenotype across a variety of human cell lines. The lux cassette was codon optimized and assembled into a synthetic human expression operon using viral 2A elements as linker regions. Human kidney, breast cancer, and colorectal cancer cell lines were both transiently and stably transfected with the humanized operon and the resulting autobioluminescent phenotype was evaluated using common imaging instrumentation. Autobioluminescent cells were screened for cytotoxic effects resulting from lux expression and their utility as bioreporters was evaluated through the demonstration of repeated monitoring of single populations over a prolonged period using both a modified E-SCREEN assay for estrogen detection and a classical cytotoxic compound detection assay for the antibiotic Zeocin. Furthermore, the use of self-directed bioluminescent initiation in response to target detection was assessed to determine its amenability towards deployment as fully autonomous sensors. In all cases, bioluminescent measurements were supported with traditional genetic and transcriptomic evaluations. Our results demonstrate that the viral 2A-linked, humanized lux genetic architecture successfully produced autobioluminescent phenotypes in all cell lines tested without the induction of cytotoxicity. This autobioluminescent phenotype allowed for repeated interrogation of populations and self-directed control of bioluminescent activation with detection limits and EC 50 values similar to traditional reporter systems, making the autobioluminescent cells amenable to automated monitoring and significantly reducing the time and cost required to perform bioluminescent workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Quantitative characterization of collagen in the fibrotic capsule surrounding implanted polymeric microparticles through second harmonic generation imaging

The collagenous capsule formed around an implant will ultimately determine the nature of its in vivo fate. To provide a better understanding of how surface modifications can alter the collagen orientation and composition in the fibrotic capsule, we used second harmonic generation (SHG) microscopy to evaluate collagen organization and structure generated in mice subcutaneously injected with chemically functionalized polystyrene particles. SHG is sensitive to the orientation of a molecule, making it a powerful tool for measuring the alignment of collagen fibers. Additionally, SHG arises from the second order susceptibility of the interrogated molecule in response to the electric field. Variation in these tensor components distinguishes different molecular sources of SHG, providing collagen type specificity. Here, we demonstrated the ability of SHG to differentiate collagen type I and type III quantitatively and used this method to examine fibrous capsules of implanted polystyrene particles. Data presented in this work shows a wide range of collagen fiber orientations and collagen compositions in response to surface functionalized polystyrene particles. Dimethylamino functionalized particles were able to form a thin collagenous matrix resembling healthy skin. These findings have the potential to improve the fundamental understanding of how material properties influence collagen organization and composition quantitatively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). Finally, when analyzing empirical data (wholegenome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Genetic interaction mapping with microfluidic-based single cell sequencing

Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms.

Science & Technology - Other Topics↗
DOE OSTI2023

Characterizing inhibitors of human AP endonuclease 1

AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg 2+ -bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Snake River Plain Geothermal Play Fairway Analysis - Volcanic Vents, Lacustrine Sediments, and post-Miocene Faults KMZ files

This dataset contain raw data files in kmz files (Google Earth georeference format). These files include volcanic vent locations and age, the distribution of fine-grained lacustrine sediments (which act as both a seal and an insulating layer for hydrothermal fluids), and post-Miocene faults compiled from the Idaho Geological Survey, the USGS Quaternary Fault database, and unpublished mapping. It also contains the Composite Common Risk Segment Map created during Phase 1 studies, as well as a file with locations of select deep wells used to interrogate the subsurface.

15 GEOTHERMAL ENERGY↗
DOE OSTI2019

PoroTomo - Distributed Temperature Sensing (DTS) Measurements made in Brady Observation Well 56-1

This submission is a follow-up to Distributed Temperature Sensing (DTS) measurements made in Brady observation well 56-1 during the PoroTomo field experiment conducted in March, 2016. The measurements in this data set were made on August 24, 2018 over an approximately 20 hour period. The fiber-optic cable extends to the bottom of the well at 367 m below the wellhead. Measurements were made with a Silixa XT DTS interrogator configured to continuously record in each file a sixty-second average of stokes and anti-stokes readings on a single channel with a bottom hole U-bend. The 2016 data were collected using a Silixia Ultima with 12.5 cm spatial sampling, whereas the XT spatial sampling interval is 25 cm with a temperature resolution of 0.03 degrees C. Raw, uncalibrated data were converted to a single .MAT file using code provided by Oregon State University's CTEMPs https://ctemps.org/data-processing. The binary Matlab file containing processed Silixa XT data is read using the Matlab statement "load('Brady_25Aug2018_ch1.mat')", which contains the arrays below. Arrays with 2361 rows represent the channels and arrays with 1210 columns represent the one-minute samples.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

EGS Collab Experiment 2: Distributed Fiber Optic Temperature Data (DTS)

Distributed fiber optic sensing was an important part of the monitoring system for EGS Collab Experiment #2. A single loop of custom fiber package was grouted into the four monitoring boreholes that bracketed the experiment volume. This fiber package contained two multi-mode fibers and four single-mode fibers. These fibers were connected to an array of fiber optic interrogator units, each targeting a different measurement. The distributed temperature system (DTS) consisted of a Silixa XT-DTS unit, connected to both ends of one of the two multi-mode fibers. This system measured absolute temperature along the entire length of fiber for the duration of the experiment at a sampling rate of approximately 10 minutes. This dataset includes both raw data in XML format from the XT-DTS, as well as a processed dataset with the sections of data pertaining only to the boreholes are extracted. We have also included a report that provides all of the relevant details necessary for users to process and interpret the data for themselves. Please read this accompanying report. If, after reading it, there are still outstanding questions, please do not hesitate to contact us. Happy processing.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Utah FORGE: Well 16B(78)-32 Distributed Temperature Sensing Data from April and May 2024

This dataset includes Neubrex Energy Services fiber optic distributed temperature sensing (DTS) data from well 16B(78)-32 during stimulation and circulation, including interaction with well 16A(78)-32, during April and May 2024. The DTS data are stored in HDF5 file format and are accompanied by a PowerPoint report on the study. All times in this dataset are in UTC. Depths are in MD relative to Kelly Bushing Height, and temperatures are in degrees Fahrenheit. All DTS measurements were made using a Yokogawa 3000DTSX Distributed Temperature Sensing Interrogator Unit, with a spatial sampling interval of 3.28 feet and a temporal sampling rate of 129 seconds. The third-party Pressure-Temperature Gauge data should be used with caution after April 20, 2024, as its performance is not considered reliable beyond this date.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Identification and time evolution of thionyl chloride (SOCl 2 ) radiolysis products

In this study, innovative solutions are needed to reduce the amount of high-level waste generated by used nuclear fuel recycling strategies to support the widespread adoption of sustainable nuclear fission energy technologies. To this end, a new sulfur chloride-based process has been developed to recycle zirconium alloy-based materials, which make up a significant fraction of high-level radioactive waste. To support the continued development of this process, we present new data on the potential reaction pathways over time of the products arising from the gamma and electron beam radiolysis of neat thionyl chloride (SOCl 2 ). Interrogation of the gamma irradiated liquid by Raman spectroscopy provided more conclusive identification of the SOCl 2 degradation products, specifically sulfur dichloride (SCl 2 ), molecular chlorine (Cl 2 ), sulfur dioxide (SO 2 ), and sulfuryl chloride (SO 2 Cl 2 ). In comparison, the high dose rate (~10 7 Gy s -1 ) electron beam irradiations formed significantly more degradation products. For both cobalt-60 gamma and electron beam irradiations, the observed degradation products were found to evolve as a function of time post-irradiation via the same reaction pathways, with indication of a solvent regeneration mechanism. These findings are fortuitous for process development, as such a mechanism would be beneficial for process longevity and cost effectiveness.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗