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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 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. Finally, the dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1

The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in the fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure–function relationships within the ADCSF in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases

While density functional theory (DFT) is often an accurate and efficient methodology for evaluating molecular properties such as energies and multipole moments, this approach often yields larger errors for response properties such as the dipole polarizability (α), which describes the tendency of a molecule to form an induced dipole moment in the presence of an electric field. In this work, we provide static α tensors (and other molecular properties such as total energy components, dipole and quadrupole moments, etc.) computed using quantum chemical (QC) and DFT methodologies for all 7,211 molecules in the QM7b database. We also provide the same quantities for the 52 molecules in the AlphaML showcase database, which includes the DNA/RNA nucleobases, uncharged amino acids, several open-chain and cyclic carbohydrates, five popular pharmaceutical molecules, and 23 isomers of C 8 H n . All QC calculations were performed using linear-response coupled-cluster theory including single and double excitations (LR-CCSD), a sophisticated approach for electron correlation, and the d-aug-cc-pVDZ basis set to mitigate basis set incompleteness error. DFT calculations employed the B3LYP and SCAN0 hybrid functionals, in conjunction with d-aug-cc-pVDZ (B3LYP and SCAN0) and d-aug-cc-pVTZ (B3LYP).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a non-model bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in non-model organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T 7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool’s utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. In conclusion, our CRISPRi tool will be useful to facilitate functional studies of this non-model organism and engineer this promising microbial chassis for lignin valorization.

09 BIOMASS FUELS↗
DOE OSTI2021

Non-monotonic magnetic anisotropy behavior as a function of adsorbate coverage in Fe ultrathin films near the spin reorientation transition

Carbon monoxide (CO) adsorption on ultrathin fcc Fe films is known to result in the rotation of magnetization from out-of-plane to in-plane. By imaging in real time the magnetic domain structure of perpendicularly magnetized Fe/(2 ML)Ni/Cu(100) films during exposure to CO, we demonstrate that the effect of adsorption on the magnetic properties occurs in two distinct stages. Initially, when CO bonds preferentially on bridge sites, perpendicular magnetic anisotropy is enhanced. Later, when on-top adsorption dominates, magnetization rotates towards in-plane in agreement with previous studies. This CO-induced spin reorientation transition (SRT) is not reversible by annealing, as CO desorption would require high temperature cycles which yield permanent structural changes in the metal films. This study demonstrates the existence of a novel non-monotonic behavior of the magnetic anisotropy as a function of adsorbate coverage. The influence of CO on ultrathin film magnetism in real time near critical points, where the anisotropy balance is extremely sensitive to small variations, reveals the previously elusive complexity of this adsorbate induced SRT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Phase-based velocity extraction method for photonic Doppler velocimetry with potential higher time resolution

We present an extension of the [Takeda et al., J. Opt. Soc. Am. 72, 156 (1982)] phase extraction method to heterodyne photonic Doppler velocimetry applications. The method yields results equivalent to those obtained by the short-time Fourier transform (STFT), while offering potential improvements in time resolution. Unlike STFT, which relies on window functions, such as the Hamming window, that emphasize central data points and diminish the influence of edges, the extended Takeda method utilizes all data uniformly. This uniform treatment allows for the derivation of empirical equations that directly relate velocity error to the actual time resolution rather than to the local analysis duration. The established equation provides a useful metric for both optimizing hardware configuration and guiding data analysis. Simulation and experimental results confirm that, for a given dataset, specifying a target time resolution yields consistent velocity errors for both methods. These findings underscore the Takeda method’s advantages, particularly its potential higher time resolution and reduced computational burden, making it a valuable tool for high-throughput applications such as laser dynamic compression experiments.

Computer simulation↗
DOE OSTI2024

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties

Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exact solution of burst pressure for thick-walled pipes using the flow theory of plasticity

This paper develops an exact solution of burst pressure for defect-free, thick-walled pipes using the flow theory of plasticity in terms of the average shear stress yield criterion (or Zhu-Leis yield criterion). The pipe steel is assumed to obey the power-law strain hardening rule, and large plastic deformation is described by the finite strain theory. On this basis, internal pressure is obtained as a power series function of the effective strains on the inside and outside surfaces of the thick-walled pipe with use of the second Bernoulli numbers. At burst failure, the Zhu-Leis flow solution of burst pressure is determined as a power series solution, and the burst effective strains, the burst effective stresses, and the burst pressure are functions of the diameter ratio (D o / D i ), strain hardening exponent (n), and ultimate tensile strength (UTS). Similarly, the Tresca and von Mises flow solutions of burst pressure are also determined as a power series solution in terms of the Tresca and von Mises yield criteria. A general closed-from exact solution of burst pressure is then proposed for the three yield criteria, and the results showed that the proposed exact solution matches well with the power series solution for each yield criterion. Moreover, the von Mises flow solution is an upper bound prediction, the Tresca flow solution is a lower bound prediction, and the Zhu-Leis flow solution is an intermediate prediction that agrees well with the finite element analysis results of burst pressure for thick-walled pipes. Furthermore, two datasets of full-scale burst tests are then utilized to evaluate and validate the proposed flow solutions of burst pressure for both thin and thick-walled pipes.

42 ENGINEERING↗
DOE OSTI2016

Dimension-independent likelihood-informed MCMC

Many Bayesian inference problems require exploring the posterior distribution of high-dimensional parameters that represent the discretization of an underlying function. This work introduces a family of Markov chain Monte Carlo (MCMC) samplers that can adapt to the particular structure of a posterior distribution over functions. Two distinct lines of research intersect in the methods developed here. First, we introduce a general class of operator-weighted proposal distributions that are well defined on function space, such that the performance of the resulting MCMC samplers is independent of the discretization of the function. Second, by exploiting local Hessian information and any associated low-dimensional structure in the change from prior to posterior distributions, we develop an inhomogeneous discretization scheme for the Langevin stochastic differential equation that yields operator-weighted proposals adapted to the non-Gaussian structure of the posterior. The resulting dimension-independent and likelihood-informed (DILI) MCMC samplers may be useful for a large class of high-dimensional problems where the target probability measure has a density with respect to a Gaussian reference measure. Two nonlinear inverse problems are used to demonstrate the efficiency of these DILI samplers: an elliptic PDE coefficient inverse problem and path reconstruction in a conditioned diffusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Comparative DFT Computational Studies with Experimental Investigations for Novel Synthesized Fluorescent Pyrazoline Derivatives

A novel series of pyrazoline derivatives were synthesized and their spectral properties were characterized via FT-IR, {sup 1}H, and {sup 13}C NMR. The electronic transitions and fluorescence properties were tracked via UV-Vis and emission spectrometry. The density functional theory (DFT) calculations have been also computed to get spot onto the geometry, electronic transitions and spectroscopic properties theoretically that has been compared with the encountered experimental ones. Moreover, the dipole moment, optimized energy, HOMO - LUMO energies and band gaps were calculated for novel candidates pyrazoline derivatives with highly fluorescence quantum yield.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Optimum plasma grid bias for a negative hydrogen ion source operation with Cs

The functions of a biased plasma grid of a negative hydrogen (H{sup −}) ion source for both pure volume and Cs seeded operations are reexamined. Proper control of the plasma grid bias in pure volume sources yields: enhancement of the extracted negative ion current, reduction of the co-extracted electron current, flattening of the spatial distribution of plasma potential across the filter magnetic field, change in recycling from hydrogen atomic/molecular ions to atomic/molecular neutrals, and enhanced concentration of H{sup −} ions near the plasma grid. These functions are maintained in the sources seeded with Cs with additional direct emission of negative ions under positive ion and neutral hydrogen bombardment onto the plasma electrode.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Nanocluster ionization energies and work function of aluminum, and their temperature dependence

Ionization threshold energies of Al{sub n} (n = 32-95) nanoclusters are determined by laser ionization of free neutral metal clusters thermalized to several temperatures in the range from 65 K to 230 K. The photoion yield curves of cold clusters follow a quadratic energy dependence above threshold, in agreement with the Fowler law of surface photoemission. Accurate data collection and analysis procedures make it possible to resolve very small (few parts in a thousand) temperature-induced shifts in the ionization energies. Extrapolation of the data to the bulk limit enables a determination of the thermal shift of the polycrystalline metal work function, found to be in excellent agreement with theoretical prediction based on the influence of thermal expansion. Small clusters display somewhat larger thermal shifts, reflecting their greater susceptibility to thermal expansion. Ionization studies of free size-resolved nanoclusters facilitate understanding of the interplay of surface, electronic, and lattice properties under contamination-free conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Participant and spectator scaling of spectator fragments in Au + Au and Cu + Cu collisions at s N N = 19.6 and 22.4 GeV

Spectator fragments resulting from relativistic heavy ion collisions, consisting of single protons and neutrons along with groups of stable nuclear fragments up to nitrogen (Z = 7), are measured in PHOBOS. These fragments are observed in Au+Au ( s N N = 19.6 GeV) and Cu+Cu (22.4 GeV) collisions at high pseudorapidity (η). The dominant multiply-charged fragment is the tightly bound helium (α), with lithium, beryllium, and boron all clearly seen as a function of collision centrality and pseudorapidity. In this paper, we observe that in Cu+Cu collisions, it becomes much more favorable for the α fragments to be released than lithium. The yields of fragments approximately scale with the number of spectator nucleons, independent of the colliding ion. The shapes of the pseudorapidity distributions of fragments indicate that the average deflection of the fragments away from the beam direction increases for more central collisions. Finally, a detailed comparison of the shapes for α and lithium fragments indicates that the centrality dependence of the deflections favors a scaling with the number of participants in the collision.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Unconventional Error Cancellation Explains the Success of Hartree–Fock Density Functional Theory for Barrier Heights

Energy barriers, which control the rates of chemical reactions, are seriously underestimated by computationally efficient semilocal approximations for the exchange-correlation energy. The accuracy of a semilocal density functional approximation is strongly boosted for reaction barrier heights by evaluating that approximation non-self-consistently on Hartree–Fock electron densities, which has been known for ~30 years. Here, the conventional explanation is that the Hartree–Fock theory yields the more accurate density. This work presents a benchmark Kohn–Sham inversion of accurate coupled-cluster densities for the reaction H 2 + F → HHF → H + HF and finds a strong, understandable cancellation between positive (excessively overcorrected) density-driven and large negative functional-driven errors (expected from stretched radical bonds in the transition state) within this Hartree–Fock density functional theory. This confirms earlier conclusions (Kaplan, A. D., et al. J. Chem. Theory Comput. 2023, 19, 532–543) based on 76 barrier heights and three less reliable, but less expensive, fully nonlocal density functional proxies for the exact density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Energy dependence of polarized 𝛾⁢𝛾 → 𝑒 + ⁢ 𝑒− in peripheral Au+Au collisions at $\sqrt{s_{NN}}$ = 54.4 and 200 GeV with the STAR experiment at RHIC

We report the differential yields at mid-rapidity of the Breit-Wheeler process (𝛾⁢𝛾 → 𝑒 + ⁢𝑒 − ) in peripheral Au+Aucollisions at $\sqrt{s_{NN}}$ = 54.4 and 200 GeV with the STAR experiment at the Relativistic Heavy Ion Collider (RHIC), as a function of energy $\sqrt{s_{NN}}$, 𝑒 + ⁢𝑒 − transverse momentum 𝑝 T , 𝑝$^{2}_{T}$, invariant mass 𝑀 𝑒⁢𝑒 , and azimuthal angle. In the invariant mass range of 0.4 < 𝑀 𝑒⁢𝑒 < 2.6GeV/𝑐 2 at low transverse momentum (𝑝 T < 0.15GeV/𝑐), the yields increase while the pair √⟨𝑝$^{2}_{T}$⟩ decreases with increasing $\sqrt{s_{NN}}$, a feature that is correctly predicted by the QED calculation. Here, the energy dependencies of the measured quantities are sensitive to the nuclear form factor, infrared divergence and photon polarization. The data are compiled and used to extract the charge radius of the Au nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Cloning and functional characterization of a p-coumaroyl quinate/shikimate 3′-hydroxylase from potato (Solanum tuberosum)

Highlights: • StC3′H catalyzed the formation of coumaroyl quinate and coumaroyl shikimate in vitro. • Antisense downregulation of StC3′H in potato tubers caused moderate increases in ferulic acid conjugates and chlorogenic acid. • A reduction in tuber yield was observed in antisense StC3′H lines, though their response to a bacterial pathogen was not significantly affected. Chlorogenic acid (CGA) plays an important role in protecting plants against pathogens and promoting human health. Although CGA accumulates to high levels in potato tubers, the key enzyme p-coumaroyl quinate/shikimate 3′-hydroxylase (C3′H) for CGA biosynthesis has not been isolated and functionally characterized in potato. In this work, we cloned StC3′H from potato and showed that it catalyzed the formation of caffeoylshikimate and CGA (caffeoylquinate) from p-coumaroyl shikimate and p-coumaroyl quinate, respectively, but was inactive towards p-coumaric acid in in vitro enzyme assays. When the expression of StC3′H proteins was blocked through antisense (AS) inhibition under the control of a tuber-specific patatin promoter, moderate changes in tuber yield as well as phenolic metabolites in the core tuber tissue were observed for several AS lines. On the other hand, the AS and control potato lines exhibited similar responses to a bacterial pathogen Pectobacterium carotovorum. These results suggest that StC3′H is implicated in phenolic metabolism in potato. They also suggest that CGA accumulation in the core tissue of potato tubers is an intricately controlled process and that additional C3′H activity may also be involved in CGA biosynthesis in potato.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Ultrafast Exciton Transport with a Long Diffusion Length in Layered Perovskites with Organic Cation Functionalization

Abstract Layered perovskites have been employed for various optoelectronic devices including solar cells and light‐emitting diodes for improved stability, which need exciton transport along both the in‐plane and the out‐of‐plane directions. However, it is not clear yet what determines the exciton transport along the in‐plane direction, which is important to understand its impact toward electronic devices. Here, by employing both steady‐state and transient photoluminescence mapping, it is found that in‐plane exciton diffusivities in layered perovskites are sensitive to both the number of layers and organic cations. Apart from exciton–phonon coupling, the octahedral distortion is revealed to significantly affect the exciton diffusion process, determined by temperature‐dependent photoluminescence, light‐intensity‐dependent time‐resolved photoluminescence, and density function theory calculations. A simple fluorine substitution to phenethylammonium for the organic cations to tune the structural rigidity and octahedral distortion yields a record exciton diffusivity of 1.91 cm 2 s −1 and a diffusion length of 405 nm along the in‐plane direction. This study provides guidance to manipulate exciton diffusion by modifying organic cations in layered perovskites.

Xiao, Xun↗