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At least 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways

Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP’s enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP’s role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex

Microhomology-mediated end joining (MMEJ), an error-prone pathway for DNA double-strand break (DSB) repair, is implicated in genomic rearrangement and oncogenic transformation; however, its contribution to repair of radiation-induced DSBs has not been characterized. We used recircularization of a linearized plasmid with 3'-P-blocked termini, mimicking those at X-ray-induced strand breaks, to recapitulate DSB repair via MMEJ or nonhomologous end-joining (NHEJ). Sequence analysis of the circularized plasmids allowed measurement of relative activity of MMEJ versus NHEJ. While we predictably observed NHEJ to be the predominant pathway for DSB repair in our assay, MMEJ was significantly enhanced in preirradiated cells, independent of their radiation-induced arrest in the G2/M phase. MMEJ activation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2), enhancing XRCC1’s interaction with the end resection enzymes MRE11 and CtIP. Both endonuclease and exonuclease activities of MRE11 were required for MMEJ, as has been observed for homology-directed DSB repair (HDR). Furthermore, the XRCC1 co-immunoprecipitate complex (IP) displayed MMEJ activity in vitro, which was significantly elevated after irradiation. Our studies thus suggest that radiation-mediated enhancement of MMEJ in cells surviving radiation therapy may contribute to their radioresistance and could be therapeutically targeted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in Chlamydomonas

Abstract Microalgae accumulate triacylglycerol (TAG) during nutrient deprivation and break it down after nutrient resupply, and these processes involve dramatic shifts in cellular carbon allocation. Due to the importance of algae in the global carbon cycle, and the potential of algal lipids as feedstock for chemical and fuel production, these processes are of both ecophysiological and biotechnological importance. However, the metabolism of TAG is not well understood, particularly the contributions of fatty acids (FAs) from different membrane lipids to TAG accumulation and the fate of TAG FAs during degradation. Here, we used isotopic labeling time course experiments on Chlamydomonas reinhardtii to track FA synthesis and transfer between lipid pools during nitrogen (N)-deprivation and resupply. When cells were labeled before N-deprivation, total levels of label in cellular FAs were unchanged during subsequent N-deprivation and later resupply, despite large fluxes into and out of TAG and membrane lipid pools. Detailed analyses of FA levels and labeling revealed that about one-third of acyl chains accumulating in TAG during N-deprivation derive from preexisting membrane lipids, and in total, at least 45% of TAG FAs passed through membrane lipids at one point. Notably, most acyl chains in membrane lipids during recovery after N-resupply come from TAG. Fluxes of polyunsaturated FAs from plastidic membranes into TAG during N-deprivation were particularly noteworthy. These findings demonstrate a high degree of integration of TAG and membrane lipid metabolism and highlight a role for TAG in storage and supply of membrane lipid components.

Plant Sciences↗
DOE OSTI2018

Tunneling topological vacua via extended operators: (Spin-)TQFT spectra and boundary deconfinement in various dimensions

Distinct quantum vacua of topologically ordered states can be tunneled into each other via extended operators. The possible applications include condensed matter and quantum cosmology. We present a straightforward approach to calculate the partition function on various manifolds and ground state degeneracy (GSD), mainly based on continuum/cochain topological quantum field theories (TQFTs), in any dimension. This information can be related to the counting of extended operators of bosonic/fermionic TQFTs. On the lattice scale, anyonic particles/strings live at the ends of line/surface operators. Certain systems in different dimensions are related to each other through dimensional reduction schemes, analogous to (de)categorification. Examples include spin TQFTs derived from gauging the interacting fermionic symmetry-protected topological states (with fermion $\mathbb Z$$f\atop{2}$) of parity symmetry groups $\mathbb Z{_4}$×$\mathbb Z{_2}$ and ($\mathbb Z{_4}$) 2 in 3+1D, also $\mathbb Z{_2}$ and ($\mathbb Z{_2}$) 2 in 2+1D. Gauging the last three cases begets non-Abelian spin TQFTs (fermionic topological order). We consider situations where a TQFT lives on (1) a closed spacetime or (2) a spacetime with a boundary, such that the bulk and boundary are fully gapped and short- or long-range entangled (SRE/LRE). Anyonic excitations can be deconfined on the boundary. We introduce new exotic topological interfaces on which neither particle nor string excitations alone condense, but only fuzzy-composite objects of extended operators can end (e.g., a string-like composite object formed by a set of particles can end on a special 2+1D boundary of 3+1D bulk). We explore the relations between group extension constructions and partially breaking constructions (e.g., 0-form/higher-form/“composite” breaking) of topological boundaries, after gauging. We comment on the implications of entanglement entropy for some such LRE systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

A bacterial flavin‐dependent oxidoreductase that captures carbon dioxide into biomass

Atmospheric carbon dioxide is used as a carbon source for building biomass in plants and photosynthetic microbes. Non‐photosynthetic processes that also fix carbon dioxide have more recently been discovered. This research focuses on a microbial mechanism for coupling acetone to CO 2 to make a central metabolite, acetoacetate. The key reaction is catalyzed by NADPH‐2‐ketopropyl‐coenzyme M oxidoreductase/carboxylase (2‐KPCC), a bacterial enzyme that is part of the flavin and cysteine‐disulfide containing oxidoreductase family (DSORs) which are best known for reducing metallic or disulfide substrates. Our research asks: how has nature repurposed a DSOR to, uniquely, break a C‐S bond and then trap and fix CO 2 ? 2‐KPCC lacks a conserved, catalytically essential acid‐base histidine possessed by all other DSOR enzymes, having instead a phenylalanine (F501) at the same position. Mutagenesis showed that a F501H mutant has a similar rate of catalytic turnover; however, the product is acetone instead of acetoacetate (Figure 1). We hypothesized that F501 is important for both the reductive half reaction – which generates the reactive, C‐S bond breaking form of the active site – and for the oxidative half, in which an enolacetone intermediate reacts with either the correct (CO 2 ) or incorrect (H + ) electrophile. In this study, we used real‐time and spectroscopic methods to examine the reductive half reaction. In typical DSORs, this reaction generates a Cys/FAD charge transfer species. However, we showed that 2‐KPCC generates an electronically unique form of the active site, in which the flavin is oxidized and a pair of active site histidines are reduced and protonated. We hypothesize that this form of the active site generates the substrate‐reactive Cys in a more nucleophilic form, where it is capable of cleaving relatively strong C‐S bonds. The resulting enolacetone carbanion is an extremely potent nucleophile that is capable of directly attacking CO 2 . Research on 2‐KPCC and other biological CO 2 fixation methods adds to our arsenal of strategies for carbon dioxide capture and use. Support or Funding Information DOE:DE‐FG02‐04ER15563 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Mattice, Jenna↗
DOE OSTI2018

Dry and hot: the hydraulic consequences of a climate change-type drought for Amazonian trees

How plants respond physiologically to leaf warming and low water availability may determine how they will perform under future climate change. In 2015-2016 an unprecedented drought occurred across Amazonia with record-breaking high temperatures and low soil moisture, offering a unique opportunity to evaluate the performances of Amazonian trees to a severe climatic event. We quantified the responses of leaf water potential, sap velocity, whole-tree hydraulic conductance (Kwt), turgor loss and xylem embolism, during and after the 2015-2016 El Niño for five canopy-tree species. Leaf/xylem safety margins (SM), sap velocity and Kwt showed a sharp drop during warm periods. SMs were negatively correlated with vapor pressure deficit but had no significant relationship with soil water storage. Based on our calculations of canopy stomatal and xylem resistances, the decrease in sap velocity and Kwt was due to a combination of xylem cavitation, and stomatal closure. Our results suggest extremely warm droughts greatly amplify the degree of trees’ physiological stress and can lead to mortality. Given the extreme nature of the 2015-2016 El Niño and that temperatures are predicted to increase, this work can serve as a case study of the possible impact climate warming can have on tropical trees.

Fontes, Clarissa G.↗
DOE OSTI2026

Electronic glasses from a broken gauge symmetry in disorder-free systems

Glass phases can be stabilized by quenched disorders, as in most spin-glass materials, or self-generated through kinetic freezing in disorder-free systems. A canonical example of the latter is structural glasses, which have been extensively studied for many decades. Yet, how the rugged energy landscape of a glass phase is spontaneously generated in disorder-free systems remains one of the key questions in glass physics. Here, in this work, we present a general electronic mechanism for the emergence of glassy phase using the example of itinerant electrons coupled to XY spins on a lattice. This model can also be viewed as the mean-field theory of a superconducting system with attractive density-density interactions. Intriguingly, the electron gauge symmetry in the strong pairing limit gives rise to a macroscopic degeneracy of XY spins. In the presence of electron hopping that breaks the gauge symmetry, the lifting of the extensive degeneracy leads to a glass phase with disordered pairings. Our findings highlight a scenario in which a glassy state originates from the breaking of quantum gauge symmetry without quenched disorders.

XY model↗
DOE OSTI2026

Ferroelectric Fractals: Switching Mechanism of Wurtzite AlN

The advent of wurtzite ferroelectrics is enabling new ferroelectric devices for computer memory that have the potential to bypass the von Neumann bottleneck due to their robust polarization and silicon compatibility. However, the atomistic switching mechanism of wurtzites is still undetermined due to the limitations of density functional theory simulation size and experimental temporal and spatial resolution. Thus, physics-informed materials engineering to reduce coercive field and breakdown in these devices has been limited. In this work, the atomistic mechanism of domain wall migration and domain growth in aluminum nitride-based wurtzites is uncovered using molecular dynamics and Monte Carlo simulations. We reveal the anomalous switching mechanism of fast 1D single columns of atoms propagating from a slow-moving 2D fractallike domain wall. We find that the critical nucleus is a single aluminum ion that breaks its bond with one nitrogen and bonds to another nitrogen; this creates a cascade that flips atoms directly only in the same column, due to the extreme locality (sharpness) of the domain walls in wurtzites. We further show how the fractallike shape of the domain wall in the 2D plane breaks assumptions in the Kolmogorov, Avrami, and Ishibashi (KAI) model and leads to the anomalously fast switching in wurtzite structured ferroelectrics.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Axion Mass Prediction from Adaptive Mesh Refinement Cosmological Lattice Simulations

The quantum chromodynamics (QCD) axion arises as the pseudo-Goldstone mode of a spontaneously broken Abelian Peccei-Quinn (PQ) symmetry. If the scale of PQ symmetry breaking occurs below the inflationary reheat temperature and the domain wall number is unity, then there is a unique axion mass that gives the observed dark matter (DM) abundance. Computing this mass has been the subject of intensive numerical simulations for decades since the mass prediction informs laboratory experiments. Axion strings develop below the PQ symmetry-breaking temperature, and as the string network evolves, it emits axions that go on to become the DM. A key ingredient in the axion mass prediction is the spectral index of axion radiation emitted by the axion strings. We compute this index in this Letter using the most precise and accurate large-scale simulations to date of the axion-string network leveraging adaptive mesh refinement to achieve the precision that would, otherwise, require a static lattice with 262,144 3 lattice sites. We find a scale-invariant axion radiation spectrum to within 1% precision and find no evidence that the spectral index of radiation evolves with time. Accounting for axion production from strings prior to the QCD phase transition leads us to predict that the axion mass should be approximately 𝑚 𝑎 ∈ (45, 65) μ ⁢eV. However, we provide preliminary evidence that axions are produced in greater quantities from the string-domain-wall network collapse during the QCD phase transition, potentially increasing the mass prediction to as much as 300 μ ⁢eV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Interfacial alloying contributions to the magnetic proximity effect in Pt/dysprosium iron garnet

The magnetic proximity effect (MPE), a magnetic response from a heavy metal layer induced by an adjacent magnetic layer, plays an important role in the behavior of heavy-metal/ferro- or ferrimagnet thin film heterostructures. However, in the case of heavy-metal/rare earth iron garnet bilayers the presence and magnitude of the MPE has been debated. We previously reported an MPE in a Pt/dysprosium iron garnet (DyIG) heterostructure where the two layers were grown without breaking vacuum, finding that the magnetic moment present in the Pt layer scales with the magnitude of the DyIG moment and varies nonmonotonically through the DyIG compensation temperature. However, the origin of the magnetic signal from the Pt layer was not identified. In contrast, Pt/DyIG grown with a vacuum break did not exhibit an MPE. Here we investigate the origin of the magnetic moment in the Pt layer using x-ray absorption spectroscopy, x-ray circular dichroism, composition mapping and simulations of ion bombardment. In conclusion, the results are consistent with the presence of an intermixed Fe-Dy-Pt interfacial alloy layer formed during the growth of the Pt on the DyIG and resulting in a measurable MPE.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Oscillation-independent probes of nonstandard neutrino interactions from supernovae

Extreme astrophysical environments provide unique laboratories for testing fundamental neutrino interactions. We present the first oscillation-independent astrophysical probe of nonstandard neutrino interactions (NSI), using coincident neutral-current signals across diverse detectors to break degeneracies that have long limited sensitivity reach. Using self-consistent NSI supernova simulations and flavor-independent neutral-current scattering we show that anticorrelated signatures between JUNO liquid scintillator and dark matter detectors such as DARWIN/XLZD, ARGO, or RES-NOVA enable clear discrimination between NSI and flavor-conversion effects. For a Galactic supernova at Betelgeuse distance our approach enables an independent probe of neutrino-quark NSI couplings in parameter space that can reach and extend beyond current terrestrial limits. This multidetector approach enables breaking degeneracies in terrestrial searches and is broadly applicable to a wide range of upcoming experiments, establishing a new principle for testing fundamental interactions with astrophysical data.

Beatty, Angela R. [San Francisco State U.; LBL, Be↗
DOE OSTI2025

Nonparametric extensions of nuclear equations of state: Probing the breakdown scale of relativistic mean-field theory

Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.

Equations of state of nuclear matter↗
DOE OSTI2025

Impact of Tiny Fermi Pockets with Extremely High Mobility on the Hall Anomaly in the Kagome Metal CsV 3 ⁢Sb 5

The kagome metal CsV 3 ⁢Sb 5 exhibits an unusual charge-density-wave (CDW) order, where the emergence of loop current order that breaks time-reversal symmetry (TRS) has been proposed. A key feature of this CDW phase is a nonmonotonic Hall effect at low fields, often attributed to TRS breaking. However, its origin remains unclear. Here, we conduct comprehensive magnetotransport measurements on CsV 3 ⁢Sb 5 and, through mobility spectrum analysis, identify the formation of tiny Fermi pockets with extremely high mobility below the CDW transition. Furthermore, electron irradiation experiments reveal that the nonmonotonic Hall effect is significantly suppressed in samples with reduced mobility, despite no substantial change in the electronic structure. In conclusion, these results indicate that the nonmonotonic Hall effect originates from these tiny Fermi pockets with high mobility carriers rather than anomalous Hall mechanisms, providing new insights into understanding the Hall anomaly in this kagome system.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Portal matter models of kinetic mixing with two light dark gauge bosons

The kinetic mixing (KM) portal mandates the existence of at least one new gauge boson, the dark photon (DP) based on the group 𝑈⁢(1) 𝐷 , which mixes with the Standard Model (SM) photon via loops of other new heavy particles carrying both SM and dark charges called portal matter (PM). Arguments exist based on the renormalization group equations running of the 𝑈⁢(1) 𝐷 gauge coupling suggesting that at higher scales 𝑈⁢(1) 𝐷 becomes part of a more complex non-Abelian group, a simple example being just the SM-like 𝐺 𝐷 =𝑆⁢𝑈⁢(2)𝐼 ×𝑈⁢(1) 𝑌 𝐼 . In our past analyses, it was always assumed that 𝐺 𝐷 broke in a SM-like manner directly to the DP’s 𝑈⁢(1) 𝐷 which then subsequently broke at low energies ≲1 GeV. However, this need not be the case, and 𝐺 𝐷 can instead break to 𝑈⁢(1) 𝑇 3⁢𝐼 ×𝑈⁢(1) 𝑌 𝐼 , with 𝑇 3⁢𝐼 being the diagonal generator of 𝑆⁢𝑈⁢(2) 𝐼 , now producing two light gauge bosons which obtain masses at the ≲1 GeV scale. In this paper, we explore the phenomenology of a very simple realization of this kind of alternative setup employing non-Abelian KM and having a minimal, leptonlike PM sector, demonstrating its distinctive nature in comparison to the previously examined symmetry breaking path. The effects of interference between these gauge bosons on thermal dark matter annihilation, the production of new heavy gauge, and Higgs and PM states at colliders, as well as the corresponding signatures for the light dark gauge bosons are examined. Collider signatures of this setup are found to be particularly challenging.

extensions of Higgs sector↗
DOE OSTI2022

Quantum simulation of quantum phase transitions using the convex geometry of reduced density matrices

Transitions of many-particle quantum systems between distinct phases at absolute-zero temperature, known as quantum phase transitions, require an exacting treatment of particle correlations. Here in this work, we present a general quantum-computing approach to quantum phase transitions that exploits the geometric structure of reduced density matrices. While typical approaches to quantum phase transitions examine discontinuities in the order parameters, the origin of phase transitions—their order parameters and symmetry breaking—can be understood geometrically in terms of the set of two-particle reduced density matrices (2-RDMs). The convex set of 2-RDMs provides a comprehensive map of the quantum system including its distinct phases as well as the transitions connecting these phases. Because 2-RDMs can potentially be computed on quantum computers at nonexponential cost, even when the quantum system is strongly correlated, they are ideally suited for a quantum-computing approach to quantum phase transitions. We compute the convex set of 2-RDMs for a Lipkin-Meshkov-Glick spin model on IBM superconducting-qubit quantum processors. Even though computations are limited to few-particle models due to device noise, comparisons with a classically solvable 1000-particle model reveal that the finite-particle quantum solutions capture the key features of the phase transitions including the strong correlation and the symmetry breaking.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Photonic-band-gap architectures for long-lifetime room-temperature polariton condensation in GaAs quantum wells

In this work, we describe AlGaAs photonic-crystal architectures that simultaneously realize strong exciton-photon coupling, long polariton lifetime, and room-temperature polariton Bose-Einstein condensation (BEC). Strong light trapping, induced by a 3D photonic band gap (PBG), leads to peak field intensity 20 times as large as that in an AlGaAs Fabry-Pérot microcavity and exciton-photon coupling as large as 20 meV (i.e., vacuum Rabi splitting 40 meV). The strong exciton-photon coupling, small polariton effective mass, and long polariton lifetime lead to possible realizations of equilibrium room-temperature BEC. We also consider the influence of polarization degeneracy and symmetry breaking in the ground state on the BEC-onset temperature and condensate fraction. Woodpile and slanted-pore PBG structures that break X-Y symmetry facilitate larger condensate fractions at moderate temperatures. The effects of electronic and photonic disorder are marginal, thanks to the 3D photonic band gap.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Broadband Nonreciprocity Enabled by Strong Coupling of Magnons and Microwave Photons

Nonreciprocity of signal transmission enhances the capacity of communication channels and protects the transmission quality against possible signal instabilities, thus becoming an important component for ensuring coherent information processing. However, nonreciprocal transmission requires breaking time-reversal symmetry (TRS), which poses challenges of both practical and fundamental character that hinder progress. Here we report an alternative scheme for achieving broadband nonreciprocity using a specially engineered hybrid microwave cavity. The TRS breaking is realized via strong coherent coupling between a selected chiral mode in the microwave cavity and a single collective spin excitation (magnon) in a ferromagnetic yttrium iron garnet sphere. The nonreciprocity in transmission is observed to span nearly a 0.5-GHz frequency band, which outperforms by two orders of magnitude the previously achieved bandwidths. Our findings suggest a promising direction for robust coherent information processing in a broad range of systems in both the classical and the quantum regime.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Phase transition preceding magnetic long-range order in the double perovskite Ba 2 NaOsO 6

Recent theoretical studies [G. Chen et al., Phys. Rev. B 82, 174440 (2010); H. Ishizuka et al., Phys. Rev. B 90, 184422 (2014)] for the magnetic Mott insulator Ba 2 NaOsO 6 have proposed a low-temperature order parameter that breaks lattice rotational symmetry without breaking time reversal symmetry, leading to a nematic phase just above the magnetic ordering temperature. We present high-resolution calorimetric and magnetization data of the same Ba 2 NaOsO 6 single crystal and show evidence for a weakly field-dependent phase transition occurring at a temperature of T s ≈ 9.5K, above the magnetic ordering temperature of T c ≈ 7.5K. This transition appears as a broadened step in the low-field temperature dependence of the specific heat. The evolution of the phase boundary with applied magnetic field suggests that this phase coincides with the phase of broken local point symmetry seen in NMR experiments at high fields [L. Lu et al., Nat. Commun. 8, 14407 (2017)]. Here, the magnetic field dependence of the specific heat provides clear indications for magnetic correlations persisting at temperatures between T c and T s where long-range magnetic order is absent, giving support for the existence of the proposed nematic phase.

36 MATERIALS SCIENCE↗

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