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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Designing Imidazolium Poly(amide-amide) and Poly(amide-imide) Ionenes and Their Interactions with Mono- and Tris(imidazolium) Ionic Liquids

Here we introduce the synthesis and thermal properties of a series of sophisticated imidazolium ionenes with alternating amide-amide or amide-imide backbone functionality, and investigate the structural effects of mono(imidazolium) and unprecedented tris(imidazolium) ionic liquids (ILs) in these ionenes. The new set of poly(amide-amide) (PAA) and poly(amide-imide) (PAI) ionenes represent the intersection of conventional high-performance polymers with the ionene archetype–presenting polymers with alternating functional and ionic elements precisely sequenced along the backbone. The effects of polymer composition on the thermal properties and morphology were analyzed. Five distinct polymer backbones were synthesized and combined with a stoichiometric equivalent of the IL 1-benzyl-3-methylimidazolium bistriflimide ([Bnmim][Tf 2 N]), which were studied to probe the self-assembly, structuring, and contributions of intermolecular forces when IL is added. Furthermore, three polyamide (PA) or polyimide (PI) ionenes with simpler xylyl linkages were interfaced with [Bnmim][Tf 2 N] as well as a novel amide-linked tris(imidazolium) IL, to demonstrate the structural changes imparted by the inclusion of functional, ionic additives dispersed within the ionene matrix. This work highlights the possibilities for utilizing concepts from small molecules which exhibit supramolecular self-assembly to guide creative design and manipulate the structuring of ionenes.

36 MATERIALS SCIENCE↗
DOE OSTI2022

NO x Control and Measurement Technology for Heavy-Duty Diesel Engines (CRADA Final Report)

The Catalyst CRADA focused on lean-NO x trap (LNT) and selective catalytic reduction (SCR) automotive emission control catalyst technology. It particularly had the goal of developing and applying advanced diagnostics capable of elucidating the network and sequence of catalyst reactions, as well as how they are affected by real-world operation and aging. Another overarching goal and action of this CRADA section was to develop methods to quantify and monitor catalyst states and support the development of full and reduced models for design and in-use control applications. William Partridge was the ORNL principal investigator (PI) throughout the Catalyst CRADA; Neal Currier was the Cummins PI through circa 2017, and Saurabh Joshi was the subsequent Cummins PI.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

UniKP: a unified framework for the prediction of enzyme kinetic parameters

Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (k cat ), Michaelis constant (K m ), and catalytic efficiency (k cat / K m ), from protein sequences and substrate structures. A two-layer framework derived from UniKP (EF-UniKP) has also been proposed to allow robust k cat prediction in considering environmental factors, including pH and temperature. In addition, four representative re-weighting methods are systematically explored to successfully reduce the prediction error in high-value prediction tasks. We have demonstrated the application of UniKP and EF-UniKP in several enzyme discovery and directed evolution tasks, leading to the identification of new enzymes and enzyme mutants with higher activity. UniKP is a valuable tool for deciphering the mechanisms of enzyme kinetics and enables novel insights into enzyme engineering and their industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

gene editing↗
DOE OSTI2022

FITEVT: A FORTRAN program for arrival-time analysis of nuclear-decay events

FITEVT is a FORTRAN program designed to analyze recorded arrival times of nuclear-decay events affected by dead-time. Here, the primary goal of the program is precise and accurate determination of half-lives. Its method involves imposition of a known sufficiently long extending dead-time to the recorded event sequence, so that the original dead-time effects are completely obliterated and the remaining live-times of the survived events are known exactly. Upon completion of the analysis, the arrival-time spectrum and the live-time spectrum are predicted and compared to those constructed from the survived events.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F 1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

Chung, Henri C.↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence P - Raw Data

Sequence P: Wake Flow Visualization, Upwind (P) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 15 m/s. Yaw angles of 0° to –60° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. The aluminum blade tip designed to contain a smoke generator was installed, and counterweights were installed in the non-instrumented blade tip to compensate. The turbine was positioned at the appropriate yaw angle, and the smoke generator was ignited remotely. The campaign duration was 3 minutes for all tests except P1000000, which was 2 minutes. The file name convention was the standard format except for P10000A0, which indicated a 3° pitch angle. File P1000000 used a 12° pitch angle. After these two campaigns were collected, it was determined that all subsequent data should be collected with a 3° pitch angle. Pressure data were not acquired during this sequence, so all associated data values were flagged as not applicable by setting the measured values in the data file to 0.000 Pa. Corresponding pressure data are available from Sequence H for the 3° pitch angle test points. Flow visualization data obtained from wall- and ceiling-mounted video cameras were recorded to videotape. The camera locations and calibration procedures are described in Appendix J.

17 WIND ENERGY↗
DOE OSTI2026

Small-Signal Stability of Grid-Forming Converters Under Fault Conditions

Threshold virtual impedance (TVI)-based current limiting for grid-forming converters (GFMs) has gained great interest due to its ability to maintain voltage source behaviour during faults. However, sequence component extraction (SCE) and negative-sequence control (NSC) are often overlooked in small-signal stability assessments during faults. This paper develops small-signal sequence impedance models for GFMs under four well-known SCE methods based on TVI current limiting control during symmetrical fault conditions. Using the developed impedance models, the impacts of SCE and NSC, and the voltage and current control loop bandwidths, on system stability during faults are investigated. Additionally, since negative-sequence TVI (TVI-) is typically added along with its positive-sequence counterpart, which is often inductive, inductive and resistive TVI- are examined. The findings suggest that a higher voltage or current control loop bandwidth has a negative impact on system stability, while SCE and NSC largely reduce the stable range for voltage and current control loop bandwidth during faults, and that the severity of such impacts is determined by the particular SCE method. Furthermore, it is observed that inductive TVI- significantly degrades system stability, while resistive TVI- can enhance stability when suitable SCE methods are appropriately selected and designed. Matlab/Simulink electromagnetic transient simulations validate these analytical results.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Next steps in high-repetition-rate laser development for Thomson scattering

Design of a next generation high-rep-rate laser system is underway, aiming for a maximum rep rate of 100 kHz for 1 ms. This will be a "pulse-burst" laser, which is a type of heat-capacity laser. Heat-capacity laser operation is characterized by a burst of pulses of limited duration, with burst length ≤100 ms and pulse rep rate ≥1 kHz. Waste heat accumulates in the laser rod during the burst. This heat is deposited evenly throughout the rod volume, with very little heat removed during the burst, such that temperature rises evenly across the rod radius. Thus beam distortion due to thermal gradients is small. Heat is removed from the rod after the burst, with typically tens of seconds between bursts. Pulse-burst operation of flashlamp pumped Nd:YAG lasers is a cost-effective route to high-rep-rate capability. Pulse-burst laser systems with "fast burst" rep rates in the range of 10–20 kHz have been built for the Thomson scattering diagnostics on MST, NSTX-U, and LHD. For Thomson scattering diagnostic application, the typical requirements are 1064 nm, 1–2 J/pulse, ≤30 ns FWHM pulse, with a top-hat beam profile. A major requirement for this next generation laser system is flexibility in burst sequence programs, ranging from 1 kHz for 100 ms to 100 kHz for 1 ms, and a variety of scenarios in between so that operation can be tailored to plasma experiment requirements. Flashlamp pumping will be used for this next generation laser because it is inexpensive and flexible. A new switch-regulated flashlamp driver will provide improved flashlamp control at lower cost. Additional design issues such as the optimum flashlamp pumping spectrum and optimum Nd doping will be addressed. The use of commercial off-the-shelf components will be maximized in this laser system so that pulse-burst systems can be developed and built by others for new applications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Regulation of L - and D -Aspartate Transport and Metabolism in Acinetobacter baylyi ADP1

Here, the regulated uptake and consumption of d-amino acids by bacteria remain largely unexplored, despite the physiological importance of these compounds. Unlike other characterized bacteria, such as Escherichia coli, which utilizes only l-Asp, Acinetobacter baylyi ADP1 can consume both d-Asp and l-Asp as the sole carbon or nitrogen source. As described here, two LysR-type transcriptional regulators (LTTRs), DarR and AalR, control d- and l-Asp metabolism in strain ADP1. Heterologous expression of A. baylyi proteins enabled E. coli to use d-Asp as the carbon source when either of two transporters (AspT or AspY) and a racemase (RacD) were coexpressed. A third transporter, designated AspS, was also discovered to transport Asp in ADP1. DarR and/or AalR controlled the transcription of aspT, aspY, racD, and aspA (which encodes aspartate ammonia lyase). Conserved residues in the N-terminal DNA-binding domains of both regulators likely enable them to recognize the same DNA consensus sequence (ATGC-N7-GCAT) in several operator-promoter regions. In strains lacking AalR, suppressor mutations revealed a role for the ClpAP protease in Asp metabolism. In the absence of the ClpA component of this protease, DarR can compensate for the loss of AalR. ADP1 consumed l- and d-Asn and l-Glu, but not d-Glu, as the sole carbon or nitrogen source using interrelated pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Restoration and Modification of Magnetosome Biosynthesis by Internal Gene Acquisition in a Magnetotactic Bacterium

We report that the Integration of a large-sized DNA fragment into a chromosome is an important strategy for characterization of cellular functions in microorganisms. Magnetotactic bacteria synthesize intracellular organelles comprising membrane-bound single crystalline magnetite, also referred to as magnetosomes. Magnetosomes have gained interest in both scientific and engineering sectors as they can be utilized as a material for biomedical and nanotechnological applications. Although genetic engineering of magnetosome biosynthesis mechanism has been investigated, the current method requires cumbersome gene preparation processes. Here, the chromosomal integration of a plasmid containing ≈27 magnetosome genes (≈26 kbp region) in a non-magnetic mutant of Magnetospirillum magneticum AMB-1 using a broad-host-range plasmid is shown. The genome sequencing of gene-complemented strains reveals the chromosomal integration of the plasmid with magnetosome genes at a specific site, most likely by catalysis of an endogenous transposase. Magnetosome production is successfully enhanced by integrating a variation of magnetosome gene operons in the chromosome. This chromosomal integration mechanism will allow the design of functional magnetosomes de novo and M. magneticum AMB-1 may be used as a chassis for the designed magnetosome production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Abstract Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

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

Large room-temperature elastocaloric effect in a bulk polycrystalline Ni-Ti-Cu-Co alloy with low isothermal stress hysteresis

Creation of high-performance advanced elastocaloric materials is essential for the execution of elastocaloric refrigeration that can be an environment-friendly and high-efficiency substitute for the widely used traditional vapor-compression cooling technology. Here we have developed a bulk polycrystalline Ni-Ti-Cu-Co shape memory alloy exhibiting large elastocaloric effect, low stress hysteresis and room temperature working temperature, all of which are of great importance to and urgently demanded for high-efficiency room-temperature elastocaloric refrigeration. This newly developed (Ni 42.5 Ti 50 Cu 7.5 ) 99 Co 1 alloy shows a large room-temperature elastocaloric effect with directly measured adiabatic temperature change up to -14.4 K during unloading. The stress hysteresis of the isothermal superelastic stress-strain curve is as low as 60 MPa when the maximum tensile strain is 2.7%. Owing to the large elastocaloric effect and low stress hysteresis, a very high coefficient of performance up to 19 is achieved on the material level. This newly developed (Ni 42.5 Ti 50 Cu 7.5 ) 99 Co 1 alloy is a robust candidate for efficient elastocaloric refrigeration. Advanced in-situ synchrotron high-energy X-ray diffraction technique was employed to reveal the phase transformation sequence and to accurately determine the crystal structure of different phases, based on which the lattice compatibility between the transforming phases was evaluated and the phase transformation strain was predicted, providing in-depth fundamental understanding of the martensitic transformation in this newly developed alloy. This work could be useful for designing high-performance elastocaloric materials for solid-state cooling applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo–electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

60 APPLIED LIFE SCIENCES↗