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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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143 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Gapless Higgs mode in the Fulde-Ferrell-Larkin-Ovchinnikov state of a superconductor

We report the Higgs mode associated with amplitude fluctuations of the superconducting gap in uniform superconductors is usually heavy, which makes its excitation and detection difficult. We report on the existence of a gapless Higgs mode in the Fulde-Ferrell-Larkin-Ovchinnikov states. This feature originates from the Goldstone mode associated with translation-symmetry breaking. The existence of the gapless Higgs mode is demonstrated by using both a phenomenological model and microscopic Bardeen-Cooper-Schrieffer (BCS) theory. The gapless Higgs mode can avoid the decay into other low-energy excitations, which renders it stable and detectable.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5–1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

NF-κB and neutrophil extracellular traps cooperate to promote breast cancer progression and metastasis

Highlights: • Cancer cells–derived factors, such as IL-8 and G-CSF, induce NETs formation via PAD4 and NF-κB. • NETs increase the interaction of NEMO with IKKα/β and enhance NF-κB activation. • Blockade of NETs using PAD4 inhibitor decreases NF-κB and tumor metastasis. • Selective inhibition of NF-κB reduces NETs formation and tumor growth and metastasis. Aberrant NF-κB activation and neutrophil extracellular traps (NETs) are associated with breast cancer progression. How NF-κB and NETs modulate each other in breast cancer development remains unclear. Here, we found that NETs induced by phorbol 12-myristate 13-acetate promote breast cancer cell progression. In turn, cancer cells–derived factors, such as IL-8 and granulocyte colony-stimulating factor, stimulate neutrophils to form NETs. Mechanistically, NETs increased the interaction of NF-κB essential modifier (NEMO) with IκB kinase (IKK)α/β and enhanced NF-κB activation. We then employed a cell-permeable peptide corresponding to the NEMO-binding domain (NBD) of IKKα/β, termed NBD peptide, which disrupts NETs-mediated NEMO interaction with IKKα/β and abolished NF-κB activation in vitro. NBD peptide also reduced IL-8 level and NETs formation, and suppressed primary tumor growth and/or lung metastasis in human breast cancer mouse xenograft models and mouse spontaneous breast cancer model. Blockade of NET formation using a peptidylarginine deiminase 4 (PAD4) pharmacologic inhibitor decreased NF-κB activation and tumor metastasis. Collectively, these data suggest that NF-κB associates with NETs to form a positive loop facilitating breast tumor progression and metastasis, and that selective inhibition of NF-κB and PAD4-dependent NETs provides an effective therapeutic approach for treating breast cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Integrated Process for Direct Air Capture of CO 2 and Electrochemical Conversion to Ethanol

This Cooperative Research and Development Agreement (CRADA) between UT-Battelle, LLC and Reactwell, L.L.C. aimed to facilitate the development of an energy-efficient and cost-effective technology that captures carbon dioxide (CO 2 ) from ambient air and converts it electrochemically to ethanol. Direct air capture (DAC) of CO 2 offers the prospect of permanently lowering the atmospheric CO 2 concentration, providing economic and energy-efficient technologies can be developed and deployed at a large scale. DAC has the potential for high-capacity atmospheric CO 2 capture, the flexibility of placement anywhere on earth, and the generation of high-purity CO 2 streams. The most significant technical challenge with DAC is the very low atmospheric concentration of CO 2 , thereby requiring sorbents that bind CO 2 quickly, strongly, and selectively against other components in the air. Integrating DAC with CO 2 conversion into useful chemicals, fuels, or materials can provide an economically feasible solution for mitigating climate change. As long as the carbon contained in these products is taken from the atmosphere and no additional carbon emissions result from their production, processing, and transportation, they can be considered carbon-neutral products. This CRADA facilitated the development of a new net-zero emission technology that closes the carbon cycle by combining DAC with the catalytic electrochemical conversion of CO 2 into ethanol.

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

Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold

Multidrug efflux is a major contributor to antibiotic resistance in Gram-negative bacterial pathogens. Inhibition of multidrug efflux pumps is a promising approach for reviving the efficacy of existing antibiotics. Previously, inhibitors targeting both the efflux transporter AcrB and the membrane fusion protein AcrA in the Escherichia coli AcrAB-TolC efflux pump were identified. In this work we use existing physicochemical property guidelines to generate a filtered library of compounds for computational docking. We then experimentally test the top candidate coumpounds using in vitro binding assays and in vivo potentiation assays in bacterial strains with controllable permeability barriers. We thus identify a new class of inhibitors of E. coli AcrAB-TolC. Six molecules with a shared scaffold were found to potentiate the antimicrobial activity of erythromycin and novobiocin in hyperporinated E. coli cells. Importantly, these six molecules were also active in wild-type strains of both Acinetobacter baumannii and Klebsiella pneumoniae, potentiating the activity of erythromycin and novobiocin up to 8-fold.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Multiomics and deep learning dissect regulatory syntax in human development

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Design of tough adhesive from commodity thermoplastics through dynamic crosslinking

Tough adhesives provide resistance against high debonding forces, and these adhesives are difficult to design because of the simultaneous requirement of strength and ductility. Here, we report a design of tough reversible/recyclable adhesive materials enabled by incorporating dynamic covalent bonds of boronic ester into commodity triblock thermoplastic elastomers that reversibly bind with various fillers and substrates. The spectroscopic measurements and density functional theory calculations unveil versatile dynamic covalent binding of boronic ester with various hydroxy-terminated surfaces such as silica nanoparticles, aluminum, steel, and glass. The designed multiphase material exhibits exceptionally high adhesion strength and work of debonding with a rebonding capability, as well as outstanding mechanical, thermal, and chemical resistance properties. Bonding and debonding at the interfaces dictate hybrid material properties, and this revelation of tailored dynamic interactions with multiple interfaces will open up a new design of adhesives and hybrid materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

An auto-inhibited state of protein kinase G and implications for selective activation

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of Bis(trifluoromethylsulfonyl)imide Interactions with Metal Cations Through a Chemical Informatics Approach

Nominally weakly coordinating anions are useful for modulating the solubility and chemical properties of metal complexes, but identification and analysis of the systematics of the interactions of anions with cationic metal complexes has not received the attention it deserves. Here, a chemical informatics approach is demonstrated for identifying and quantitatively analyzing the ways that the bis(trifluoromethylsulfonyl)imide anion (TFSI) can interact with metal-containing species. An open access computer program (PyCIFTer) was developed to facilitate large-scale structural analysis of TFSI-containing species by utilization of experimental atomic coordinate data from single-crystal X-ray diffraction (XRD) studies obtained from the Cambridge Structural Database (CSD). PyCIFTer establishes a three-dimensional vector space from the raw atomic coordinates, generating acyclic, undirected graphs that are used to rapidly analyze the structural properties (bond lengths and angles) of TFSI in individual structures in sequential/batch fashion. The structures are sorted by PyCIFTer into groups based on pre-set and chemically sensible criteria, affording a comprehensive and systematic view of TFSI structural chemistry. This approach avoids tedious one-at-a-time interrogation of structures, a prospect unreasonable in this case, and many others of contemporary chemical relevance; there were over 1500 structures in the CSD containing TFSI as of November 2024. The results demonstrate that TFSI only rarely binds to cations in the solid state, favoring the formation of species in which TFSI is found in cations’ outer coordination spheres. The prospect of applying PyCIFTer to other moieties is also discussed. PyCIFTer is also schematically compared to the commercial CSD Python application programming interface (API). Taken together, this work demonstrates the usefulness of modular workflows for sequential/batch analysis of structural data from XRD, an approach that appears poised to accelerate the translation of legacy structural results into new chemical insights and hypotheses.

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

Search for a Nonrelativistic Boson in Two-Body Antimuon Decay

We demonstrate the feasibility of probing the charged lepton-flavor-violating decay μ + → e + X 0 for the presence of a slow-moving neutral boson X 0 capable of undergoing gravitational binding to large structures and, as such, able to participate in some cosmological scenarios. A short exposure to surface antimuons from beam line M20 at TRIUMF generates a branching ratio limit of ≲ 10 –5 . This is comparable to or better than previous searches for this channel, although in a thus-far-unexplored region of X 0 phase space very close to the kinematic limit of the decay, where m X 0 approaches m μ+ . The future improved sensitivity of the method using a customized p -type point-contact germanium detector is described.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Cooperative Atomically Dispersed Fe–N 4 and Sn–N x Moieties for Durable and More Active Oxygen Electroreduction in Fuel Cells

One grand challenge for deploying porous carbons with embedded metal–nitrogen–carbon (M–N–C) moieties as platinum group metal (PGM)-free electrocatalysts in proton-exchange membrane fuel cells is their fast degradation and inferior activity. Here, we report the modulation of the local environment at Fe–N 4 sites via the application of atomic Sn–N x sites for simultaneously improved durability and activity. We discovered that Sn–N x sites not only promote the formation of the more stable D2 FeN 4 C 10 sites but also invoke a unique D3 SnN x –Fe II N 4 site that is characterized by having atomically dispersed bridged Sn–N x and Fe–N 4 . This new D3 site exhibits significantly improved stability against demetalation and several times higher turnover frequency for the oxygen reduction reaction (ORR) due to the shift of the reaction pathway from a single-site associative mechanism to a dual-site dissociative mechanism with the adjacent Sn site facilitating a lower overpotential cleavage of the O–O bond. This mechanism bypasses the formation of the otherwise inevitable intermediate that is responsible for demetalation, where two hydroxyl intermediates bind to one Fe site. Lastly, a mesoporous Fe/Sn-PNC catalyst exhibits a positively shifted ORR half-wave potential and more than 50% lower peroxide formation. This, in combination with the stable D3 site and enriched D2 Fe sites, significantly enhanced the catalyst’s durability as demonstrated in membrane electrode assemblies using complementary accelerated durability testing protocols.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Node Distortions in UiO-66 Inform Negative Thermal Expansion Mechanisms: Kinetic Effects, Frustration, and Lattice Hysteresis

In metal–organic frameworks (MOFs) the interplay between the dynamics of individual components and how these are constrained by the extended lattice can yield unusual emergent phenomena. For the archetypal Zr-MOF, UiO-66, we explore the cooperative dynamics of a Zr-node transformation that gives rise to negative thermal expansion (NTE). Here, using in situ synchrotron X-ray scattering, with powder diffraction and pair distribution function (PDF) analyses, we identify lattice hysteresis and a thermal ramp-rate-dependence of the thermal expansion. Specifically, kinetic trapping of distorted node states formed at high temperature, leads to broad variability in the apparent thermal expansion which ranges from large positive to large negative thermal expansion with coefficients of thermal expansion (CTE) from +45 to –80 × 10 –6 K –1 . Time-resolved relaxation studies at selected temperatures suggest that when equilibrated UiO-66 is intrinsically NTE, with a CTE of –35 × 10 –6 K –1 . Kinetic trapping of the node-distorted state following high temperature activation has broad implications for characterization and applications of these Zr-MOFs; the nonequilibrium node state depends on the thermal history of the sample with quench vs slow cooling likely to impact gas binding, pore volume, and accessible catalytic sites.

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

Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma

When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ 2 C 2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Coexistence of Bulk-Nodal and Surface-Nodeless Cooper Pairings in a Superconducting Dirac Semimetal

The interplay of nontrivial topology and superconductivity in condensed matter physics gives rise to exotic phenomena. However, materials are extremely rare where it is possible to explore the full details of the superconducting pairing. Here, we investigate the momentum dependence of the superconducting gap distribution in a novel Dirac material PdTe. Using high resolution, low temperature photoemission spectroscopy, we establish it as a spin-orbit coupled Dirac semimetal with the topological Fermi arc crossing the Fermi level on the (010) surface. This spin-textured surface state exhibits a fully gapped superconducting Cooper pairing structure below $T_{c}$ ~ 4.5 K. Moreover, we find a node in the bulk near the Brillouin zone boundary, away from the topological Fermi arc. In conclusion, these observations not only demonstrate the band resolved electronic correlation between topological Fermi arc states and the way it induces Cooper pairing in PdTe, but also provide a rare case where surface and bulk states host a coexistence of nodeless and nodal gap structures enforced by spin-orbit coupling.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Discrete Open-Shell Tris(bipyridinium radical cationic) Inclusion Complexes in the Solid State

In the solid state the properties of organic radicals depend heavily on radical-radical interactions that are influenced by the superstructure of the crystalline phase. Here, we report the synthesis and characterization of a substituted tetracationic cyclophane, cyclobis(paraquat-p-1,4- dimethoxyphenylene), and outline how its bisradical dicationic redox state associates with the methyl viologen radical cation (MV •+ ) to give a trisradical tricationic inclusion complex. The (super)structures of the reduced cyclophane and this 1:1 complex in the solid-state deviate from the analogous (super)structures observed for the reduced state of cyclobis(paraquat-p-phenylene) and that of its trisradical tricationic complex. Titration experiments with a range of guests reveal that the methoxy substituents on the para-xylenyl do not influence significantly of the binding affinity of the cyclophane for small neutral guests, whereas the affinity decreases by an order of magnitude for larger radical cationic guests such as MV •+ . X-Ray diffraction reveals that the solid- state structures of the tricationic trisradical complexes to be a discrete entity with weak intermolecular orbital overlap between the neighboring complexes. Transient nutation EPR experiment and DFT calculations confirm that the complex has a doublet spin configuration in the ground state as a result of the strong orbital overlap within the complex, while the quartet-state spin configuration is higher in energy and so is inaccessible at ambient temperature. The superconducting quantum interference device (SQUID) measurement reveals that trisradical tricationic complexes interact antiferromagnetically (J/k = - 2.33 K) and form a 1D Heisenberg antiferromagnetic chain along the a-axis in the crystal. Furthermore, these results offer new insights into the design and synthesis of organic magnetic materials based on host-guest inclusion complexes.

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

Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides

Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB–TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.

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

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗