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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

Abstract MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.

Science & Technology - Other Topics↗
DOE OSTI2026

Structural basis for the subtype-selectivity of K Ca 2.2 channel activators

Small-conductance (K Ca 2.2) and intermediate-conductance (K Ca 3.1) Ca 2+ -activated K + channels are gated by a Ca 2+ -calmodulin dependent mechanism. NS309 potentiates the activity of both K Ca 2.2 and K Ca 3.1, while rimtuzalcap selectively activates K Ca 2.2. Rimtuzalcap has been used in clinical trials for the treatment of spinocerebellar ataxia and essential tremor. We report cryo-electron microscopy structures of NS309-bound K Ca 2.2 and K Ca 3.1, in addition to structures of rimtuzalcap-bound K Ca 2.2 and mutant K Ca 3.1_R355K. The different conformations of calmodulin and the cytoplasmic HC helices in the two channels underlie the subtype-selectivity of rimtuzalcap for K Ca 2.2. NS309 binds to pre-existing pockets in both channels, while the bulkier rimtuzalcap binds in an induced-fit pocket in K Ca 2.2 requiring conformational changes. In K Ca 2.2, calmodulin’s N-lobes are sufficiently far apart to enable conformational changes to accommodate either NS309 or rimtuzalcap. In K Ca 3.1, calmodulin’s N-lobes are closer to each other and constrained by K Ca 3.1’s HC helices, which allows binding of NS309 but not rimtuzalcap. Replacement of arginine-355 in K Ca 3.1’s HB helix with lysine (K Ca 3.1_R355K) allows the binding of rimtuzalcap and renders the mutant channel sensitive to rimtuzalcap. These structures provide a framework for structure-based drug design targeting K Ca 2.2 channels.

Nam, Young-Woo [Chapman Univ., Irvine, CA (United ↗
DOE OSTI2025

Uncertainty quantification for misspecified machine learned interatomic potentials

The use of high-dimensional regression techniques from machine learning has significantly improved the quantitative accuracy of interatomic potentials. Atomic simulations can now plausibly target quantitative predictions in a variety of settings, which has brought renewed interest in robust means to quantify uncertainties. In many practical settings where model complexity is constrained (e.g., due to performance considerations), misspecification — the inability of any one choice of model parameters to exactly match all training data — is a key contributor to errors that is often disregarded. Here, we employ a recent misspecification-aware regression technique to quantify parameter uncertainties, which is then propagated to a broad range of phase and defect properties in tungsten. The propagation is performed through both brute-force resampling and implicit Taylor expansion. The propagated misspecification uncertainties robustly quantify and bound errors on a broad range of material properties. We demonstrate application to recent foundational machine learning interatomic potentials, accurately predicting and bounding errors in MACE-MPA-0 energy predictions across the diverse materials project database.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Approximate symmetries and quantum error correction

Abstract Quantum error correction (QEC) is a key concept in quantum computation as well as many areas of physics. There are fundamental tensions between continuous symmetries and QEC. One vital situation is unfolded by the Eastin–Knill theorem, which forbids the existence of QEC codes that admit transversal continuous symmetry actions (transformations). Here, we systematically study the competition between continuous symmetries and QEC in a quantitative manner. We first define a series of meaningful measures of approximate symmetries motivated from different perspectives, and then establish a series of trade-off bounds between them and QEC accuracy utilizing multiple different methods. Remarkably, the results allow us to derive general quantitative limitations of transversally implementable logical gates, an important topic in fault-tolerant quantum computation. As concrete examples, we showcase two explicit types of quantum codes, obtained from quantum Reed–Muller codes and thermodynamic codes, respectively, that nearly saturate our bounds. Finally, we discuss several potential applications of our results in physics.

Physics↗
DOE OSTI2022

Unconventional excitonic states with phonon sidebands in layered silicon diphosphide

Complex correlated states emerging from many-body interactions between quasiparticles (electrons, excitons and phonons) are at the core of condensed matter physics and material science. In low-dimensional materials, quantum confinement affects the electronic, and subsequently, optical properties for these correlated states. Here, by combining photoluminescence, optical reflection measurements and ab initio theoretical calculations, we demonstrate an unconventional excitonic state and its bound phonon sideband in layered silicon diphosphide (SiP 2 ), where the bound electron–hole pair is composed of electrons confined within one-dimensional phosphorus–phosphorus chains and holes extended in two-dimensional SiP 2 layers. The excitonic state and emergent phonon sideband show linear dichroism and large energy redshifts with increasing temperature. Our ab initio many-body calculations confirm that the observed phonon sideband results from the correlated interaction between excitons and optical phonons. With these results, we propose layered SiP2 as a platform for the study of excitonic physics and many-particle effects.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Lattice distortion inducing exciton splitting and coherent quantum beating in CsPbI 3 perovskite quantum dots

It is well known that shape or crystal anisotropy in nanocrystal quantum dots, which are tiny semiconductor nanoparticles, results in energy splitting of their optically bright excitons (bound electron-hole pairs), which is known as fine structure splitting (FSS). Studying FSS usually requires single or just a few quantum dots because of its sensitivity to nanocrystal size and shape. In this work, by using ensemble-level femtosecond polarized transient absorption, the authors observed clear bright-exciton FSS in solution-processed CsPbI 3 perovskite QDs, which is manifested as exciton quantum beats (periodic oscillations of kinetic traces). Remarkably, the beat frequency of a given sample, as determined by the FSS energy, can be continuously controlled by changing the temperature. The FSS is linked experimentally for the first time to temperature dependent lattice distortion in the orthorhombic crystal structure. Because these orthorhombic-phase nanocrystal quantum dots are bounded by the pseudocubic family of crystal planes, the lattice distortion results in a misalignment between the lattice vectors and the nanocrystal edge directions which breaks the symmetry, leading to previously unrecognized avoided crossing “fine-structure gap” between bright exciton. Furthermore, this fine structure gap is responsible for the ability to observe quantum beats despite the shape inhomogeneity within the measured ensemble. Lattice-distortion dependent FSS in CsPbI 3 QDs has important consequences for their application as a platform for coherence and entanglement control in quantum information science.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Magnetically confined surface and bulk excitons in a layered antiferromagnet

The discovery of two-dimensional van der Waals magnets has greatly expanded our ability to create and control nanoscale quantum phases. A unique capability emerges when a two-dimensional magnet is also a semiconductor that features tightly bound excitons with large oscillator strengths that fundamentally determine the optical response and are tunable with magnetic fields. Here, in this study, we report a previously unidentified type of optical excitation-a magnetic surface exciton-enabled by the antiferromagnetic spin correlations that confine excitons to the surface of CrSBr. Magnetic surface excitons exhibit stronger Coulomb attraction, leading to a higher binding energy than excitons confined in bulk layers, and profoundly alter the optical response of few-layer crystals. Distinct magnetic confinement of surface and bulk excitons is established by layer- and temperature-dependent exciton reflection spectroscopy and corroborated by ab initio many-body perturbation theory calculations. By quenching interlayer excitonic interactions, the antiferromagnetic order of CrSBr strictly confines the bound electron-hole pairs within the same layer, regardless of the total number of layers. Our work unveils unique confined excitons in a layered antiferromagnet, highlighting magnetic interactions as a vital approach for nanoscale quantum confinement, from few layers to the bulk limit.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural basis of the activation of a metabotropic GABA receptor

Metabotropic γ-aminobutyric acid receptors (GABA B ) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that range from addiction to psychosis. GABA B belongs to class C of the G-protein-coupled receptors, and its functional entity comprises an obligate heterodimer that is composed of the GB1 and GB2 subunits. Each subunit possesses an extracellular Venus flytrap domain, which is connected to a canonical seven-transmembrane domain. In this paper we present four cryo-electron microscopy structures of the human full-length GB1–GB2 heterodimer: one structure of its inactive apo state, two intermediate agonist-bound forms and an active form in which the heterodimer is bound to an agonist and a positive allosteric modulator. The structures reveal substantial differences, which shed light on the complex motions that underlie the unique activation mechanism of GABA B . Our results show that agonist binding leads to the closure of the Venus flytrap domain of GB1, triggering a series of transitions, first rearranging and bringing the two transmembrane domains into close contact along transmembrane helix 6 and ultimately inducing conformational rearrangements in the GB2 transmembrane domain via a lever-like mechanism to initiate downstream signalling. This active state is stabilized by a positive allosteric modulator binding at the transmembrane dimerization interface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Diversity-oriented synthesis of polymer membranes with ion solvation cages

Microporous polymers feature shape-persistent free volume elements (FVEs), which are permeated by small molecules and ions when used as membranes for chemical separations, water purification, fuel cells, and batteries. It remains a significant challenge to identify FVEs with analyte specificity, due to difficulties in generating microporous polymer libraries with sufficient diversity for screening their properties. Here, we describe a diversity-oriented synthetic (DOS) strategy for microporous polymer membranes from which we identified those whose FVEs serve as solid solvation cages for lithium ions (Li + ). Furthermore, key elements of our strategy included diversification of bis(catechol)-type monomers via multi-component Mannich reactions to introduce Li+-coordinating functionality within individual FVEs, topology-enforcing polymerizations for generating macromolecular skeletal diversity for networking FVEs into different pore architectures, and several classes of on-polymer reactions for diversifying pore geometries and dielectric properties. Lead candidate polymer membranes featuring explicit ion solvation cages exhibited both higher ionic conductivity and higher cation transference number than control membranes where FVEs were aspecific, which indicates conventional bounds for membrane permeability and selectivity for ion transport can be overcome.4 These advantages are tied to enhanced Li + partitioning from the electrolyte when the cages are present, higher diffusion barriers for anions within the pores, and network-enforced restrictions on the number of solvent molecules bound to Li+ by comparison to the bulk electrolyte, which reduces the effective mass of the working ion. Such membranes show promise as anode-stabilizing interlayers in high-voltage lithium-metal batteries for electric mobility.

42 ENGINEERING↗
DOE OSTI2023

Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence

Abstract cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection 1–3 . In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP–AMP (cGAMP) 4,5 , which leads to the expression of antimicrobial genes 6,7 . In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered 8–11 . These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3 , which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively 8,12 . Although these proteins are required to prevent infection of some bacteriophages 8 , the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.

Science & Technology - Other Topics↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging

Abstract Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca 2+ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca 2+ concentration using fluorescence lifetime imaging microscopy (FLIM).

Biochemistry & Molecular Biology↗
DOE OSTI2020

Effects of chronic low-dose radiation on cataract prevalence and characterization in wild boar (Sus scrofa) from Fukushima, Japan

This study evaluated cataracts in wild boar exposed to chronic low-dose radiation. We examined wild boar from within and outside the Fukushima Exclusion Zone for nuclear, cortical, and posterior subcapsular (PSC) cataracts in vivo and photographically. Plausible upper-bound, lifetime radiation dose for each boar was estimated from radioactivity levels in each animal’s home range combined with tissue concentrations of 134+137Cesium. Fifteen exposed and twenty control boar were evaluated. There were no significant differences in overall prevalence or score for cortical or PSC cataracts between exposed and control animals. Nuclear (centrally located) cataracts were significantly more prevalent in exposed boar (p<0.05) and had statistically higher median scores. Plausible upper-bound, lifetime radiation dose ranged from 1 to 1,600 mGy in exposed animals, with no correlation between dose and cortical or PSC score. While radiation dose and nuclear score were positively associated, the impact of age could not be completely separated from the relationship. Additionally, the clinical significance of even the highest scoring nuclear cataract was negligible. Based on the population sampled, wild boar in the Fukushima Exclusion Zone do not have a significantly higher prevalence or risk of cortical or PSC cataracts compared to control animals.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi

Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Plasma screening in mid-charged ions observed by K-shell line emission

Dense plasma environment affects the electronic structure of ions via variations of the microscopic electrical fields, also known as plasma screening. This effect can be either estimated by simplified analytical models, or by computationally expensive and to date unverified numerical calculations. We have experimentally quantified plasma screening from the energy shifts of the bound-bound transitions in matter driven by the x-ray free electron laser (XFEL). This was enabled by identification of detailed electronic configurations of the observed Kα, Kβ and Kγ lines. This work paves the way for improving plasma screening models including connected effects like ionization potential depression and continuum lowering, which will advance the understanding of atomic physics in the Warm Dense Matter regime.

Physics - Plasma physics↗
DOE OSTI2025

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.

Gonzales, Juliet (ORCID:0000000327219566)↗
DOE OSTI2020

Nature of the spin resonance mode in CeCoIn 5

Spin-fluctuation-mediated unconventional superconductivity can emerge at the border of magnetism, featuring a superconducting order parameter that changes sign in momentum space. Detection of such a sign-change is experimentally challenging, since most probes are not phase-sensitive. The observation of a spin resonance mode (SRM) from inelastic neutron scattering is often seen as strong phase-sensitive evidence for a sign-changing superconducting order parameter, by assuming the SRM is a spin-excitonic bound state. Here we show that for the heavy fermion superconductor CeCoIn 5 , its SRM defies expectations for a spin-excitonic bound state, and is not a manifestation of sign-changing superconductivity. Instead, the SRM in CeCoIn 5 likely arises from a reduction of damping to a magnon-like mode in the superconducting state, due to its proximity to magnetic quantum criticality. Our findings emphasize the need for more stringent tests of whether SRMs are spin-excitonic, when using their presence to evidence sign-changing superconductivity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗