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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 19 records
All sourcesNASA NTRSDOE OSTI
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 OSTI2021

Controlling Amphiphilic Polymer Folding beyond the Primary Structure with Protein-Mimetic Di(Phenylalanine)

While methods for polymer synthesis have proliferated, their functionality pales in comparison to natural biopolymers–strategies are limited for building the intricate network of noncovalent interactions necessary to elicit complex, protein-like functions. Using a bioinspired di(phenylalanine) acrylamide (FF) monomer, we explored the impact of various noncovalent interactions in generating ordered assembled structures. Amphiphilic copolymers were synthesized that exhibit β-sheet-like local structure upon collapsing into single-chain assemblies in aqueous environments. Here, the systematic analysis of a series of amphiphilic copolymers illustrated that the global collapse is primarily driven by hydrophobic forces. Hydrogen-bonding and aromatic interactions stabilize local structure, as β-sheet-like interactions were identified via circular dichroism and thioflavin T fluorescence. Similar analysis of phenylalanine (F) and alanine-phenylalanine acrylamide (AF) copolymers found that distancing the aromatic residue from the polymer backbone is sufficient to induce β-sheet-like local structure akin to the FF copolymers; however, the interactions between AF subunits are less stable than those formed by FF. Further, hydrogen-bond donating hydrophilic monomers disrupt internal structure formed by FF within collapsed assemblies. Collectively, these results illuminate design principles for the facile incorporation of multiple facets of protein-mimetic, higher-order structure within folded synthetic polymers.

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

Structural and Electronic Complexities of a Sulfur‐Bridged Di‐Iron Complex Composed of Mono‐ and Di‐Nitrosyl Units

The delocalized, thermodynamically stable cation, [(N 2 S 2 )Fe(NO)•Fe(NO) 2 ] + , an adduct of mono-nitrosyl and dinitrosyl iron units, is analyzed to address the unusual stability of the sulfur-bridged diiron complex in its three overall redox levels, +, 0, and −. X-ray diffraction and myriad spectroscopic techniques probe products of sequential electron uptake in the corresponding neutral and anionic species. Conundrums include unified blueshifts of the overall 3-band, ν(NO), pattern with added electrons. One-electron reduction changes the anti-ferromagnetically coupled, S = 0, cationic diiron species to the neutral analog, S = ½, with unpaired spin mainly localized on the MNIU, which decreases its ∠Fe–N–O angle by 10 degrees in response to the extra electron density. Subsequent reduction to the anionic species, S = 1, involves a major geometric change at the MNIU, which moves the Fe in {Fe(NO)} 8 out of the N 2 S 2 plane. Site-specific 15 N labeling of nitrosyl in the MNIU confirms the IR analysis and shows rapid NO exchange between the MNIU/DNIU (mono-nitrosyl iron unit/dinitrosyl iron unit) pairs during its synthesis at RT. Mössbauer spectroscopy, S K-edge XAS, and molecular orbital calculations confirm the ability of NO and the versatility of sulfur bridges to buffer and distribute electrons, a key to their major importance in metalloenzymes.

DNIC↗
DOE OSTI2022

A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 1

We report di-isobutylene has received significant attention as a promising fuel blendstock, as it can be synthesized via biological routes and is a short-listed molecule from the Co-Optima initiative. Di-isobutylene is also popularly used as an alkene representative in multi-component surrogate models for engine studies of gasoline fuels. However, there is limited experimental data available in the literature for neat di-isobutylene under engine-like conditions. Hence, most existing di-isobutylene models have not been extensively validated, particularly at lower temperatures (< 1000 K). Most gasoline surrogate models include the di-isobutylene sub-mechanism published by Metcalfe et al. with little or no modification. The current study is undertaken to develop a detailed kinetic model for di-isobutylene and validate the model using a wide range of relevant experimental data. Part 1 of this study exclusively focuses on the low- to intermediate temperature kinetics of di-isobutylene. An upcoming part 2 discusses the high-temperature model development and validation of the relevant experimental targets. Ignition delay time measurements for the di-isobutylene isomers were performed at pressures ranging from 15 - 30 bar at equivalence ratios of 0.5, 1.0, and 2.0 diluted in air and in the temperature range 650 - 900 K using two independent rapid compression machine facilities. In addition, measurements of species identified during the oxidation of these isomers were performed in a jet-stirred reactor and in a rapid compression machine. A detailed kinetic model for the di-isobutylene isomers is developed to capture the wide range of new experimental targets. For the first time, a comprehensive low-temperature chemistry submodel is included. The differences in the important reaction pathways for the accurate prediction of the oxidation of the two DIB isomers are compared using reaction path analysis. In conclusion, the most sensitive reactions controlling the ignition delay times of the DIB isomers under the pressure and temperature conditions necessary for autoignition in engines are identified.

09 BIOMASS FUELS↗
DOE OSTI2021

Evolution of a σ–(c-di-GMP)–anti-σ switch

Filamentous actinobacteria of the genus Streptomyces have a complex lifecycle involving the differentiation of reproductive aerial hyphae into spores. We recently showed c-di-GMP controls this transition by arming a unique anti-σ, RsiG, to bind the sporulation-specific σ, WhiG. The Streptomyces venezuelae RsiG–(c-di-GMP) 2 –WhiG structure revealed that a monomeric RsiG binds c-di-GMP via two E(X) 3 S(X) 2 R(X) 3 Q(X) 3 D repeat motifs, one on each helix of an antiparallel coiled-coil. Here we show that RsiG homologs are found scattered throughout the Actinobacteria. Strikingly, RsiGs from unicellular bacteria descending from the most basal branch of the Actinobacteria are small proteins containing only one c-di-GMP binding motif, yet still bind their WhiG partners. Our structure of a Rubrobacter radiotolerans (RsiG) 2 –(c-di-GMP) 2 –WhiG complex revealed that these single-motif RsiGs are able to form an antiparallel coiled-coil through homodimerization, thereby allowing them to bind c-di-GMP similar to the monomeric twin-motif RsiGs. Further data show that in the unicellular actinobacterium R. radiotolerans , the (RsiG) 2 –(c-di-GMP) 2 –WhiG regulatory switch controls type IV pilus expression. Phylogenetic analysis indicates the single-motif RsiGs likely represent the ancestral state and an internal gene-duplication event gave rise to the twin-motif RsiGs inherited elsewhere in the Actinobacteria. Thus, these studies show how the anti-σ RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP binding motifs, which functions as a monomer. Consistent with this, our structures reveal potential selective advantages of the monomeric twin-motif anti-σ factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The multifaceted role of c-di-AMP signaling in the regulation of Porphyromonas gingivalis lipopolysaccharide structure and function

This study unveils the intricate functional association between cyclic di-3’,5’-adenylic acid (c-di-AMP) signaling, cellular bioenergetics, and the regulation of lipopolysaccharide (LPS) profile in Porphyromonas gingivalis, a Gram-negative obligate anaerobe considered as a keystone pathogen involved in the pathogenesis of chronic periodontitis. Previous research has identified variations in P. gingivalis LPS profile as a major virulence factor, yet the underlying mechanism of its modulation has remained elusive. We employed a comprehensive methodological approach, combining two mutants exhibiting varying levels of c-di-AMP compared to the wild type, alongside an optimized analytical methodology that combines conventional mass spectrometry techniques with a novel approach known as FLAT n . We demonstrate that c-di-AMP acts as a metabolic nexus, connecting bioenergetic status to nuanced shifts in fatty acid and glycosyl profiles within P. gingivalis LPS. Notably, the predicted regulator gene cdaR, serving as a potent regulator of c-di-AMP synthesis, was found essential for producing N-acetylgalactosamine and an unidentified glycolipid class associated with the LPS profile. The multifaceted roles of c-di-AMP in bacterial physiology are underscored, emphasizing its significance in orchestrating adaptive responses to stimuli. Furthermore, our findings illuminate the significance of LPS variations and c-di-AMP signaling in determining the biological activities and immunostimulatory potential of P. gingivalis LPS, promoting a pathoadaptive strategy. The study expands the understanding of c-di-AMP pathways in Gram-negative species, laying a foundation for future investigations into the mechanisms governing variations in LPS structure at the molecular level and their implications for host-pathogen interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP

Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental regulators, BldD and WhiG. Here we show that c-di-GMP also binds the glycogen-debranching-enzyme, GlgX, uncovering a direct link between c-di-GMP and glycogen metabolism in bacteria. Further, we show c-di-GMP binding is required for GlgX activity. We describe structures of apo and c-di-GMP-bound GlgX and, strikingly, their comparison shows c-di-GMP induces long-range conformational changes, reorganizing the catalytic pocket to an active state. Glycogen is an important glucose storage compound that enables animals to cope with starvation and stress. Our in vivo studies reveal the important biological role of GlgX in Streptomyces glucose availability control. Overall, we identify a function of c-di-GMP in controlling energy storage metabolism in bacteria, which is widespread in Actinobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Di-nucleons do not form bound states at heavy pion mass

We perform a high-statistics lattice QCD calculation of the low-energy two-nucleon scattering amplitudes. To address discrepancies in the literature, the calculation is performed at a heavy pion mass in the limit that the light quark masses are equal to the physical strange quark mass, 𝑚 𝜋 = 𝑚 𝐾 ≃ 714 MeV. Using a state-of-the-art momentum space method, we rule out the presence of a bound di-nucleon in both the isospin 0 (deuteron) and 1 (di-neutron) channels, in contrast with many previous results that made use of compact hexaquark creation operators. To diagnose the discrepancy, we add such hexaquark interpolating operators to our basis and find that they do not affect the determination of the two-nucleon finite-volume spectrum, and thus they do not couple to deeply bound di-nucleons that are missed by the momentum-space operators. Furthermore, we perform a high-statistics calculation of the HAL QCD potential on the same gauge ensembles and find qualitative agreement with our main results. We conclude that di-nucleons do not form bound states at heavy pion masses and that previous identification of deeply bound di-nucleons must have arisen from a misidentification of the spectrum from off-diagonal elements of a correlation function.

Physics - Physics of elementary particles and fiel↗
DOE OSTI2022

A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 2

A wide variety of high temperature experimental data obtained in this study complement the data on the oxidation of the two di-isobutylene isomers presented in Part I and offers a basis for an extensive validation of the kinetic model developed in this study. Due to the increasing importance of unimolecular decomposition reactions in high-temperature combustion, we have investigated the di-isobutylene isomers in high dilution utilizing a pyrolysis microflow reactor and detected radical intermediates and stable products using vacuum ultraviolet (VUV) synchrotron radiation and photoelectron photoion coincidence (PEPICO) spectroscopy. Additional speciation data at oxidative conditions were also recorded utilizing a plug flow reactor at atmospheric pressure in the temperature range 725-1150 K at equivalence ratios of 1.0 and 3.0 and at residence times of 0.35 s and 0.22 s, respectively. Combustion products were analyzed using gas chromatography (GC) and mass spectrometry (MS). Ignition delay time measurements for di-isobutylene were performed at pressures of 15 and 30 bar at equivalence ratios of 0.5, 1.0, and 2.0 diluted in 'air' in the temperature range 900-1400 K using a high-pressure shock-tube facility. New measurements of the laminar burning velocities of di-isobutylene/air flames are also presented. The experiments were performed using the heat flux method at atmospheric pressure and initial temperatures of 298-358 K. Moreover, data consistency was assessed with the help of analysis of the temperature and pressure dependencies of laminar burning velocity measurements, which was interpreted using an empirical power-law expression. Electronic structure calculations were performed to compute the energy barriers to the formation of many of the product species formed. The predictions of the present mechanism were found to be in adequate agreement with the wide variety of experimental measurements performed.

09 BIOMASS FUELS↗
DOE OSTI2020

Reconstruction and identification of boosted di-τ systems in a search for Higgs boson pairs using 13 TeV proton-proton collision data in ATLAS

In this paper, a new technique for reconstructing and identifying hadronically decaying τ+τ- pairs with a large Lorentz boost, referred to as the di-τ tagger, is developed and used for the first time in the ATLAS experiment at the Large Hadron Collider. A benchmark di-τ tagging selection is employed in the search for resonant Higgs boson pair production, where one Higgs boson decays into a boosted $b\overline b$ pair and the other into a boosted τ+τ- pair, with two hadronically decaying τ-leptons in the final state. Using 139 fb -1 of proton-proton collision data recorded at a centre-of-mass energy of 13 TeV, the efficiency of the di-τ tagger is determined and the background with quark- or gluon-initiated jets misidentified as di-τ objects is estimated. The search for a heavy, narrow, scalar resonance produced via gluon-gluon fusion and decaying into two Higgs bosons is carried out in the mass range 1–3 TeV using the same dataset. No deviations from the Standard Model predictions are observed, and 95% confidence-level exclusion limits are set on this model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Di-nucleons do not form bound states at heavy pion mass

We perform a high-statistics lattice QCD calculation of the low-energy two-nucleon scattering amplitudes. In order to address discrepancies in the literature, the calculation is performed at a heavy pion mass in the limit that the light quark masses are equal to the physical strange quark mass, $m_π= m_K \simeq 714 $ MeV. Using a state-of-the-art momentum space method, we rule out the presence of a bound di-nucleon in both the isospin 0 (deuteron) and 1 (di-neutron) channels, in contrast with many previous results that made use of compact hexaquark creation operators. In order to diagnose the discrepancy, we add such hexaquark interpolating operators to our basis and find that they do not affect the determination of the two-nucleon finite volume spectrum, and thus they do not couple to deeply bound di-nucleons that are missed by the momentum-space operators. Further, we perform a high-statistics calculation of the HAL QCD potential on the same gauge ensembles and find qualitative agreement with our main results. We conclude that two-nucleons do not form bound states at heavy pion masses and that previous identification of deeply bound di-nucleons must have arisen from a misidentification of the spectrum from off-diagonal elements of a correlation function.

FOS: Physical sciences↗
DOE OSTI2026

Probing gluon saturation with forward di-hadron correlations in proton-nucleus collisions

We present a detailed numerical investigation of semi-inclusive forward di-hadron production in proton–nucleus collisions employing the Color Glass Condensate effective theory. We focus on the regime where di-hadrons are produced nearly back-to-back in the transverse plane, thereby justifying a transverse-momentum-dependent factorization approach in terms of small-x gluon distributions. Our computation integrates several key elements: i) non-linear rapidity evolution via the Balitsky–Kovchegov equation with running coupling, ii) both perturbative and non-perturbative Sudakov resummation, and iii) a phenomenologically constrained model for the initial conditions for small-x gluon distributions. We compare this phenomenological framework to experimental data from the STAR Collaboration on azimuthal correlations in forward di-pion production in both proton–proton and proton–gold collisions. We analyze the systematic theoretical uncertainties associated with the saturation scales of nuclei at the initial scale for rapidity evolution and with those associated with the hadronization process. Finally, we make predictions for the kinematics anticipated to be covered by the ALICE Forward Calorimeter (FoCal) upgrade at the Large Hadron Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Search for a bound di-neutron by comparing 3 He(e,e'p)d and 3 H(e,e'p)X measurements

We report on a search for a bound di-neutron by comparing electron-induced proton-knockout $(e,e'p)$ measurements from Helium-3 ($^3$He) and Tritium ($^3$H). The measurements were performed at Jefferson Lab Hall A with a 4.326 GeV electron beam, and kinematics of large momentum transfer $Q^2 \approx 1.9$ (GeV/$c$)$^2$ and $x_B>1$, to minimize contributions from non quasi-elastic (QE) reaction mechanisms. Analyzing the measured $^3$He missing mass ($M_{miss}$) and missing energy ($E_{miss}$) distributions, we can distinguish the two-body break-up reaction, in which the residual proton-neutron system remains bound as a deuteron. In the $^3$H mirror case, under the exact same kinematic conditions, we do not identify a signature for a bound di-neutron with similar binding energy to that of the deuteron. We calculate exclusion limits as a function of the di-neutron binding energy and find that, for binding equivalent to the deuteron, the two-body break-up cross section on $^3$H is less than 0.9% of that on $^3$He in the measured kinematics at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Description of di-hadron saturation signals within a universal nuclear parton distribution function approach

Di-hadron and di-jet correlation measurements in proton-nucleus (𝑝+𝐴) and electron-nucleus collisions are widely motivated as sensitive probes of novel, nonlinear quantum chromodynamices saturation dynamics in hadrons, which are particularly accessible in the dense nuclear environment at low values of Bjorken-𝑥 (𝑥 A ). Current measurements at the BNL Relativistic Heavy Ion Collider (RHIC) and the CERN Large Hadron Collider (LHC) observe a significant suppression in the per-trigger yield at forward rapidities compared to that in proton-proton collisions, nominally consistent with the “mono-jet” production expected in a saturation scenario. However, the width of the azimuthal correlation remains unmodified, in contradiction to the qualitative expectations from this physics picture. I investigate whether the construction of these observables leaves them sensitive to effects from simple nuclear shadowing as captured by, for example, universal nuclear parton distribution function (nPDF) analyses. I find that modern nPDF sets, informed by recent precision measurements sensitive to the shadowing of low-𝑥 A gluon densities in LHC and other data, can describe all or the majority of the di-hadron/jet suppression effects in 𝑝+𝐴 data at both RHIC and the LHC, while giving a natural explanation for why the azimuthal correlation width is unmodified. Notably, this is achieved via a (𝑥 A ,𝑄 2 )-differential suppression of overall cross sections only, without requiring additional physics dynamics which alter the interevent correlations.

Jets & heavy flavor physics↗
DOE OSTI2022

Prospects for Higgs and di-Higgs measurements at the ATLAS experiment

The large dataset of about 3000 {fb}^{-1} f b − 1 that will be collected at the High Luminosity LHC (HL-LHC) will be used to measure Higgs boson processes in detail. This large dataset will also provide sensitivity to di-Higgs processes and will allow for the improvement of the constraints on the Higgs boson self coupling. Studies based on current ATLAS analyses using LHC Run 2 data have been carried out to understand the expected precision and limitations of the Higgs and di-Higgs measurements at the HL-LHC. This paper presents the ATLAS prospects for Higgs and di-Higgs results at the HL-LHC.

Betti, Alessandra↗
DOE OSTI2023

Di-CNN: Domain-Knowledge-Informed Convolutional Neural Network for Manufacturing Quality Prediction

In manufacturing, convolutional neural networks (CNNs) are widely used on image sensor data for data-driven process monitoring and quality prediction. However, as purely data-driven models, CNNs do not integrate physical measures or practical considerations into the model structure or training procedure. Consequently, CNNs’ prediction accuracy can be limited, and model outputs may be hard to interpret practically. This study aims to leverage manufacturing domain knowledge to improve the accuracy and interpretability of CNNs in quality prediction. A novel CNN model, named Di-CNN, was developed that learns from both design-stage information (such as working condition and operational mode) and real-time sensor data, and adaptively weighs these data sources during model training. It exploits domain knowledge to guide model training, thus improving prediction accuracy and model interpretability. A case study on resistance spot welding, a popular lightweight metal-joining process for automotive manufacturing, compared the performance of (1) a Di-CNN with adaptive weights (the proposed model), (2) a Di-CNN without adaptive weights, and (3) a conventional CNN. The quality prediction results were measured with the mean squared error (MSE) over sixfold cross-validation. Model (1) achieved a mean MSE of 6.8866 and a median MSE of 6.1916, Model (2) achieved 13.6171 and 13.1343, and Model (3) achieved 27.2935 and 25.6117, demonstrating the superior performance of the proposed model.

47 OTHER INSTRUMENTATION↗