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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Tracing the transient reaction kinetics of adsorbed species by in situ/operando infrared spectroscopy

The dynamic reaction behavior (i.e., transient responses) of IR-observable adsorbed species and gaseous products obtained from transient kinetic studies provide valuable kinetic and mechanistic information, namely: the abundance of active intermediates and their reactivity distribution, the chemical structure of IR-observable active and spectator species, the sequence of their formation, and the kinetically significant and rate-determining step under reaction conditions of practical catalysis. We discuss the use of transient response data to elucidate the reaction mechanisms of several gas-solid reactions: CO/H 2 , CO/H 2 /C 2 H 4 , photocatalytic oxidation of ethanol, and the CO 2 -amine reaction. The IR coupled with transient kinetic techniques is especially useful for investigating the mechanisms of photocatalytic reactions because both photogenerated electrons and many adsorbed species are IR-active (exhibiting measurable IR bands), and their evolution occurs on a time scale of seconds at ambient temperature. We highlight the key features and limitations of in situ IR with transient kinetics, as well as their significance in catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

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

Efficiency of charge transfer in changing the dissociation dynamics of OD + transients formed after the photo-fragmentation of D 2 O

Here, we present an investigation of the relaxation dynamics of deuterated water molecules after direct photo-double ionization at 61 eV. We focus on the very rare D + + O + + D reaction channel in which the sequential fragmentation mechanisms were found to dominate the dynamics. Aided by theory, the state-selective formation and breakup of the transient OD + (a 1 Δ, b 1 Σ + ) is traced, and the most likely dissociation path—OD + : a 1 Δ or b 1 Σ + → A 3 Π → X 3 Σ – → B 3 Σ – —involving a combination of spin–orbit and non-adiabatic charge transfer transitions is determined. The multi-step transition probability of this complex transition sequence in the intermediate fragment ion is directly evaluated as a function of the energy of the transient OD + above its lowest dissociation limit from the measured ratio of the D + + O + + D and competing D + + D + + O sequential fragmentation channels, which are measured simultaneously. Our coupled-channel time-dependent dynamics calculations reproduce the general trends of these multi-state relative transition rates toward the three-body fragmentation channels.

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

Vaccine Advances against Venezuelan, Eastern, and Western Equine Encephalitis Viruses

Vaccinations are a crucial intervention in combating infectious diseases. The three neurotropic Alphaviruses, Eastern (EEEV), Venezuelan (VEEV), and Western (WEEV) equine encephalitis viruses, are pathogens of interest for animal health, public health, and biological defense. In both equines and humans, these viruses can cause febrile illness that may progress to encephalitis. Currently, there are no licensed treatments or vaccines available for these viruses in humans. Experimental vaccines have shown variable efficacy and may cause severe adverse effects. Here, we outline recent strategies used to generate vaccines against EEEV, VEEV, and WEEV with an emphasis on virus-vectored and plasmid DNA delivery. Despite candidate vaccines protecting against one of the three viruses, few studies have demonstrated an effective trivalent vaccine. We evaluated the potential of published vaccines to generate cross-reactive protective responses by comparing DNA vaccine sequences to a set of EEEV, VEEV, and WEEV genomes and determining the vaccine coverages of potential epitopes. Finally, we discuss future directions in the development of vaccines to combat EEEV, VEEV, and WEEV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Scout Benchmark Scenarios for U.S. Building Energy and CO2 Emissions to 2050

Overview and Intended Use Cases: These scenarios establish a range of futures for U.S. buildings sector energy use and CO2 emissions to 2050 using Scout (scout.energy.gov), a reproducible and granular model of U.S. building energy use, emissions, and consumer costs developed by the U.S. national labs for the U.S. Department of Energy's Building Technologies Office (BTO). Scout benchmark scenario data are suitable for the following example use cases: setting high-level policy goals for the U.S. buildings sector to 2050 (e.g., X% building CO2 emissions reductions vs. 2005 levels by 2030, Y% reductions vs. 2005 levels by 2050); exploring the effects of key dynamics driving U.S. buildings sector energy and CO2 emissions to 2050 that could be affected by policy levers (e.g., raising minimum technology performance levels; accelerating electrification and/or retrofit rates; introducing breakthrough technologies to the market); determining priority segments (regions, building types, and end use/technology types) and sequencing of U.S. buildings sector energy and CO2 emissions reductions to 2050 under a given set of assumptions; and/or identifying the energy and emissions impacts or cost effectiveness of specific technologies or operational approaches of interest—in isolation or after considering competition with other measures in a scenario portfolio. Scenario Summary: A total of 8 scenarios explore the effects of changes across both the demand- and supply-side of building energy use on annual U.S. building energy use and CO2 emissions from 2022–2050. Scenarios are organized into three groups representing low, moderate, and best-case potentials for building decarbonization, respectively.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Validation of Maui PSCAD Model: Motivation, Methodology, and Lessons Learned: Preprint

As power systems become increasingly dependent on inverter-based resources, the dominant physical and control interactions that determine system stability may no longer be accurately captured in positive sequence dynamic simulation tools; electromagnetic transient (EMT) simulations may be needed. This paper describes the process of creating and validating an EMT model of the entire Maui island transmission system in PSCAD software. The model is validated against the utility's PSSE model and against field data for an event that consisted of a single-phase fault followed by a generation trip. The methodology and lessons learned are summarized here.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

High-resolution crystal structure of the Borreliella burgdorferi PlzA protein in complex with c-di-GMP: new insights into the interaction of c-di-GMP with the novel xPilZ domain

ABSTRACT In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Here, we present the crystal structure of PlzA in complex with c-di-GMP (1.6 Å resolution). This is the first structure of a xPilz domain in complex with c-di-GMP to be determined. PlzA has a two-domain structure, where each domain comprises topologically equivalent PilZ domains with minimal sequence identity but remarkable structural similarity. The c-di-GMP binding site is formed by the linker connecting the two domains. While the structure of apo PlzA could not be determined, previous fluorescence resonance energy transfer data suggest that apo and holo forms of the protein are structurally distinct. The information obtained from this study will facilitate ongoing efforts to identify the molecular mechanisms of PlzA-mediated regulation in ticks and mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7±19.1 and 36.5±10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

XMM-Newton and TESS observations of the highly variable polar V496 UMa

We studied the temporal and spectral behavior of V496 UMa from the optical to the X-ray regimes. Methods. We used archival XMM-Newton and TESS observations obtained in 2017 and 2019, respectively, to perform a spectral and timing analysis of the highly variable magnetic CV. Results. The light curves of the TESS and XMM-Newton satellites reveal a double-humped pattern modulated with the periodicity of 91.058467 ± 0.00001 min. V496 UMa displays a two-pole accretion geometry in the high accretion state. X-ray spectra from these regions are composed of thermal plasma radiation and soft blackbody components with almost identical temperatures and a total accretion rate of $\dot{M}$ = 1.4(8) × 10 -11 M ⊙ yr -1 . The X-ray centers of the humps show longitudinal shifts of -18° and 4°, and shifts around photometric phase zero of -172° and -186°, for the main hump and second hump, respectively. The long-term ZTF light curves reveal high and low accretions states. Low-state ZTF and SDSS photometric data are consistent with an 0.8 M ⊙ white dwarf at 10 000 K and a main-sequence donor star with a spectral type of M5.0 at a Gaia determined distance of 758 pc. Conclusions. V496 UMa is a very bright polar in X-rays when it is in the high state. Due to its unusual geometric structure, mass accretion onto the second accretion pole is interrupted occasionally. This discontinuous behavior does not follow a certain pattern in time and has been observed so far only in the high state. The X-ray light curves display clear evidence of an accretion stream at the photometric phase of φ = 0.81, which does not show up in optical light curves. An accurate period was derived using the combined TESS and XMM-Newton data, which differs by 3.8 σ from published results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

High-throughput spin-bath characterization of spin defects in semiconductors

Detailed knowledge of the local environments of spin defects in semiconductors, such as nitrogenvacancy (NV) centers in diamond or divacancies in silicon carbide, is crucial for optimizing control and entanglement protocols in quantum sensing and information applications. However, at present a direct experimental characterization of individual defect environments is not scalable, as conventional spin-bath measurements are time consuming and difficult to automate. Achieving high-throughput characterization requires short experiments to probe the spin bath. However, with fewer and noisier measurements, the inverse problem of recovering spin-bath properties from measured data becomes ill posed, with multiple spin baths having a high likelihood of yielding the same data. In this work, we present a set of computational tools to resolve the ill-posed inverse problem of recovering the atomic positions and hyperfine couplings of random nuclei surrounding spin defects from sparse, noisy experimental coherence data, which can be obtained in hours. Here, we use a trans-dimensional Bayesian approach that incorporates ab initio data to yield full posterior distributions over nuclear spin environments, enabling robust recovery from limited data. We also provide practical tools and guidelines to determine the limits of detectability for hyperfine couplings under specific dynamical decoupling sequences and sampling conditions. In addition, we demonstrate how the tools developed here, in combination with ab initio simulations of spin baths, can guide the design of efficient experimental protocols for application-specific high-throughput screening. To showcase the utility of our approach, we apply it to design fast dynamical decoupling experiments to characterize the spin baths often individual NV centers in diamond. While the primary focus is on accelerating spin-bath characterization of spin defects, this Bayesian approach also lays the foundation for digital-twin studies of spin defects, where a virtual model of the spin-defect system evolves in real time with ongoing experimental measurements. Together, the set of tools we designed and applied paves the way for scalable deployment of spin defects in semiconductors for quantum sensing and information applications.

Bayesian methods↗
DOE OSTI2022

De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.

Chu, Alexander E.↗
DOE OSTI2023

Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Bacterial diversity↗
DOE OSTI2021

Photo Doppler Velocimetry and Gamma/Neutron Yield Measurements of Godiva-IV Critical Assembly

The purpose of this experiment was to collect data for a dynamic benchmark of the Godiva-IV burst assembly. Data were taken using two different measurement systems. The gamma & neutron flux was measured using a calibrated, high-dynamic-range scintillator detector, the MHD-240. The measurement will be used to determine the total fission yield and alpha throughout the burst and shutdown sequence of Godiva-IV. The Photon Doppler Velocimetry (PDV) measurement detected the surface motion of the burst assembly as a function of time. The combined data will be used in a multi-physics simulation of the Godiva-IV burst assembly.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

The Binary INformation from Open Clusters Using SEDs (BINOCS) Project: Reliable Photometric Mass Determinations of Binary Star Systems in Clusters

We introduce a new binary detection technique, Binary INformation from Open Clusters using SEDs (binocs), which we show is able to determine reliable stellar multiplicity and masses over a much larger mass range than current approaches. This new technique determines accurate component masses of binary and single systems of the open clusters’ main sequence by comparing observed magnitudes from multiple photometric filters to synthetic star spectral energy distributions (SEDs), allowing us to systematically probe the binary population for low-mass stars in clusters for eight well-studied open clusters. We provide new deep, infrared photometric catalogs (1.2–8.0 μm) for the key open clusters NGC 1960 (M36), NGC 2099 (M37), NGC 2420, and NGC 2682 (M67), using observations from NOAO/NEWFIRM and Spitzer/IRAC. Using these deep multiwavelength catalogs, the binocs method is applied to these clusters to determine accurate component masses for unresolved cluster binaries. We explore binary fractions as a function of cluster age, Galactic location, and metallicity.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Phase-sensitive γ-encoded recoupling of heteronuclear dipolar interactions and 1 H chemical shift anisotropy

γ-encoded recoupling sequences are known to produce strong amplitude modulations that lead to sharp doublets when Fourier transformed. These doublets depend very little on the recoupled tensor asymmetry and thus enable for the straightforward determination of dynamic order parameters. It can, however, be difficult to measure small anisotropies, or small order parameters, using such sequences; the resonances from the doublet may overlap with each other, or with the zero-frequency glitch. This limitation has prevented the widespread use of 1 H chemical shift anisotropy (CSA) for the measurement of dynamics, particularly for CH protons which typically have CSAs of only a few ppm when immobile. In this work, we introduce a simple modification to the traditional 1 H CSA and proton-detected local field pulse sequences that enables the acquisition of a hypercomplex dataset and the removal of the uncorrelated magnetization that results in the zero-frequency glitch. These new sequences then yield a frequency shift in the indirect dimension, rather than a splitting, which is easily identifiable even in cases of weak interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗