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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evidence for 4e charge of Cooper quartets in a biased multi-terminal graphene-based Josephson junction

Abstract In a Josephson junction (JJ) at zero bias, Cooper pairs are transported between two superconducting contacts via the Andreev bound states (ABSs) formed in the Josephson channel. Extending JJs to multiple superconducting contacts, the ABSs in the Josephson channel can coherently hybridize Cooper pairs among different superconducting electrodes. Biasing three-terminal JJs with antisymmetric voltages, for example, results in a direct current (DC) of Cooper quartet (CQ), which involves a four-fermion entanglement. Here, we report half a flux periodicity in the interference of CQ formed in graphene based multi-terminal (MT) JJs with a magnetic flux loop. We observe that the quartet differential conductance associated with supercurrent exhibits magneto-oscillations associated with a charge of 4 e , thereby presenting evidence for interference between different CQ processes. The CQ critical current shows non-monotonic bias dependent behavior, which can be modeled by transitions between Floquet-ABSs. Our experimental observation for voltage-tunable non-equilibrium CQ-ABS in flux-loop-JJs significantly extends our understanding of MT-JJs, enabling future design of topologically unique ABS spectrum.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Instabilities of heavy magnons in an anisotropic magnet

Abstract The search for new elementary particles is one of the most basic pursuits in physics, spanning from subatomic physics to quantum materials. Magnons are the ubiquitous elementary quasiparticle to describe the excitations of fully-ordered magnetic systems. But other possibilities exist, including fractional and multipolar excitations. Here, we demonstrate that strong quantum interactions exist between three flavors of elementary quasiparticles in the uniaxial spin-one magnet FeI 2 . Using neutron scattering in an applied magnetic field, we observe spontaneous decay between conventional and heavy magnons and the recombination of these quasiparticles into a super-heavy bound-state. Akin to other contemporary problems in quantum materials, the microscopic origin for unusual physics in FeI 2 is the quasi-flat nature of excitation bands and the presence of Kitaev anisotropic magnetic exchange interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Atomically precise engineering of spin–orbit polarons in a kagome magnetic Weyl semimetal

Atomically precise defect engineering is essential to manipulate the properties of emerging topological quantum materials for practical quantum applications. However, this remains challenging due to the obstacles in modifying the typically complex crystal lattice with atomic precision. Here, we report the atomically precise engineering of the vacancy-localized spin–orbit polarons in a kagome magnetic Weyl semimetal Co 3 Sn 2 S 2 , using scanning tunneling microscope. We achieve the step-by-step repair of the selected vacancies, leading to the formation of artificial sulfur vacancies with elaborate geometry. We find that that the bound states localized around these vacancies undergo a symmetry dependent energy shift towards Fermi level with increasing vacancy size. As the vacancy size increases, the localized magnetic moments of spin–orbit polarons become tunable and eventually become itinerantly negative due to spin–orbit coupling in the kagome flat band. These findings provide a platform for engineering atomic quantum states in topological quantum materials at the atomic scale.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Hund’s coupling mediated multi-channel quantum phase transition of a single magnetic impurity in Fe(Se, Te)

Understanding the interplay between individual magnetic impurities and superconductivity is crucial for bottom-up construction of novel phases of matter. Sub-gap bound states that are used in this endeavor are typically considered as independent entities that each result from the exchange scattering between the respective impurity orbitals and electrons of the superconducting condensate. Here we present experimental evidence of individual multi-spin impurities where the sub-gap states are not independent. Specifically, we find that by tuning the energy of the state closest to zero through zero, all other sub-gap states change particle-hole asymmetry as well. We show that this can be understood by including Hund’s coupling, which favors high-spin configurations, into a multi-orbital Anderson model. Unlike for the case of independent spins, the transition we observe signals the simultaneous departure of more than one quasiparticle from the impurity, while the parity of the ground state may remain unchanged. Our results show that Hund’s coupling is not only crucial in generating high-spin impurities, but also to understand the transition between two distinct ground states, and should therefore be taken into account for e.g. impurity-based band-structure engineering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Trapping light in air with membrane metasurfaces for vibrational strong coupling

Optical metasurfaces can manipulate electromagnetic waves in unprecedented ways at ultra-thin engineered interfaces. Specifically, in the mid-infrared (mid-IR) region, metasurfaces have enabled numerous biochemical sensing, spectroscopy, and vibrational strong coupling (VSC) applications via enhanced light-matter interactions in resonant cavities. However, mid-IR metasurfaces are usually fabricated on solid supporting substrates, which degrade resonance quality factors (Q) and hinder efficient sample access to the near-field electromagnetic hotspots. Besides, typical IR-transparent substrate materials with low refractive indices, such as CaF 2 , NaCl, KBr, and ZnSe, are usually either water-soluble, expensive, or not compatible with low-cost mass manufacturing processes. Here, we present novel free-standing Si-membrane mid-IR metasurfaces with strong light-trapping capabilities in accessible air voids. We employ the Brillouin zone folding technique to excite tunable, high-Q quasi-bound states in the continuum (qBIC) resonances with our highest measured Q-factor of 722. Leveraging the strong field localizations in accessible air cavities, we demonstrate VSC with multiple quantities of PMMA molecules and the qBIC modes at various detuning frequencies. Our new approach of fabricating mid-IR metasurfaces into semiconductor membranes enables scalable manufacturing of mid-IR photonic devices and provides exciting opportunities for quantum-coherent light-matter interactions, biochemical sensing, and polaritonic chemistry. The authors introduce a mid-IR metasurface fabricated by decorating a free-standing Si-membrane with air holes. The enhanced light-matter interactions in such air cavities enable vibrational strong coupling and advanced biochemical sensing.

infrared spectroscopy↗
DOE OSTI2020

Highly skewed current–phase relation in superconductor–topological insulator–superconductor Josephson junctions

Three-dimensional topological insulators (TIs) in proximity with superconductors are expected to exhibit exotic phenomena, such as topological superconductivity (TSC) and Majorana-bound states (MBS), which may have applications in topological quantum computation. In superconductor–TI–superconductor Josephson junctions, the supercurrent versus the phase difference between the superconductors, referred to as the current–phase relation (CPR), reveals important information including the nature of the superconducting transport. Here, we study the induced superconductivity in gate-tunable Josephson junctions (JJs) made from topological insulator BiSbTeSe 2 with superconducting Nb electrodes. We observe highly skewed (non-sinusoidal) CPR in these junctions. The critical current, or the magnitude of the CPR, increases with decreasing temperature down to the lowest accessible temperature ( T ~ 20 mK), revealing the existence of low-energy modes in our junctions. The gate dependence shows that close to the Dirac point the CPR becomes less skewed, indicating the transport is more diffusive, most likely due to the presence of electron/hole puddles and charge inhomogeneity. Our experiments provide strong evidence that superconductivity is induced in the highly ballistic topological surface states (TSS) in our gate-tunable TI-based JJs. Furthermore, the measured CPR is in good agreement with the prediction of a model which calculates the phase-dependent eigenstate energies in our system, considering the finite width of the electrodes, as well as the TSS wave functions extending over the entire circumference of the TI.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The asymmetry of antimatter in the proton

The fundamental building blocks of the proton—quarks and gluons—have been known for decades. However, we still have an incomplete theoretical and experimental understanding of how these particles and their dynamics give rise to the quantum bound state of the proton and its physical properties, such as its spin1. The two up quarks and the single down quark that comprise the proton in the simplest picture account only for a few per cent of the proton mass, the bulk of which is in the form of quark kinetic and potential energy and gluon energy from the strong force2. An essential feature of this force, as described by quantum chromodynamics, is its ability to create matter–antimatter quark pairs inside the proton that exist only for a very short time. Their fleeting existence makes the antimatter quarks within protons difficult to study, but their existence is discernible in reactions in which a matter–antimatter quark pair annihilates. In this picture of quark–antiquark creation by the strong force, the probability distributions as a function of momentum for the presence of up and down antimatter quarks should be nearly identical, given that their masses are very similar and small compared to the mass of the proton. Here we provide evidence from muon pair production measurements that these distributions are considerably different, with more abundant down antimatter quarks than up antimatter quarks over a wide range of momenta. These results are expected to revive interest in several proposed mechanisms for the origin of this antimatter asymmetry in the proton that had been disfavoured by previous results, and point to future measurements that can distinguish between these mechanisms.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1,2,3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Additionally, newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Publisher Correction: The asymmetry of antimatter in the proton

The fundamental building blocks of the proton—quarks and gluons—have been known for decades. However, we still have an incomplete theoretical and experimental understanding of how these particles and their dynamics give rise to the quantum bound state of the proton and its physical properties, such as its spin1. The two up quarks and the single down quark that comprise the proton in the simplest picture account only for a few per cent of the proton mass, the bulk of which is in the form of quark kinetic and potential energy and gluon energy from the strong force2. An essential feature of this force, as described by quantum chromodynamics, is its ability to create matter–antimatter quark pairs inside the proton that exist only for a very short time. Their fleeting existence makes the antimatter quarks within protons difficult to study, but their existence is discernible in reactions in which a matter–antimatter quark pair annihilates. In this picture of quark–antiquark creation by the strong force, the probability distributions as a function of momentum for the presence of up and down antimatter quarks should be nearly identical, given that their masses are very similar and small compared to the mass of the proton3. Here we provide evidence from muon pair production measurements that these distributions are considerably different, with more abundant down antimatter quarks than up antimatter quarks over a wide range of momenta. These results are expected to revive interest in several proposed mechanisms for the origin of this antimatter asymmetry in the proton that had been disfavoured by previous results4, and point to future measurements that can distinguish between these mechanisms.

Dove, J.↗
DOE OSTI2022

Measured proton electromagnetic structure deviates from theoretical predictions

The visible world is founded on the proton, the only composite building block of matter that is stable in nature. Consequently, understanding the formation of matter relies on explaining the dynamics and the properties of the proton’s bound state. A fundamental property of the proton involves the response of the system to an external electromagnetic field. It is characterized by the electromagnetic polarizabilities that describe how easily the charge and magnetization distributions inside the system are distorted by the electromagnetic field. Moreover, the generalized polarizabilities map out the resulting deformation of the densities in a proton subject to an electromagnetic field. They disclose essential information about the underlying system dynamics and provide a key for decoding the proton structure in terms of the theory of the strong interaction that binds its elementary quark and gluon constituents. Of particular interest is a puzzle in the electric generalized polarizability of the proton that remains unresolved for two decades. Here we report measurements of the proton’s electromagnetic generalized polarizabilities at low four-momentum transfer squared. We show evidence of an anomaly to the behaviour of the proton’s electric generalized polarizability that contradicts the predictions of nuclear theory and derive its signature in the spatial distribution of the induced polarization in the proton. Here, the reported measurements suggest the presence of a new, not-yet-understood dynamical mechanism in the proton and present notable challenges to the nuclear theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Observing the onset of pressure-driven K-shell delocalization

The gravitational pressure in many astrophysical objects exceeds one gigabar (one billion atmospheres), creating extreme conditions where the distance between nuclei approaches the size of the K shell. This close proximity modifies these tightly bound states and, above a certain pressure, drives them into a delocalized state. Both processes substantially affect the equation of state and radiation transport and, therefore, the structure and evolution of these objects. Still, our understanding of this transition is far from satisfactory and experimental data are sparse. Here, in this work, we report on experiments that create and diagnose matter at pressures exceeding three gigabars at the National Ignition Facility where 184 laser beams imploded a beryllium shell. Bright X-ray flashes enable precision radiography and X-ray Thomson scattering that reveal both the macroscopic conditions and the microscopic states. The data show clear signs of quantum-degenerate electrons in states reaching 30 times compression, and a temperature of around two million kelvins. At the most extreme conditions, we observe strongly reduced elastic scattering, which mainly originates from K-shell electrons. We attribute this reduction to the onset of delocalization of the remaining K-shell electron. With this interpretation, the ion charge inferred from the scattering data agrees well with ab initio simulations, but it is significantly higher than widely used analytical models predict.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

High-temperature 205 Tl decay clarifies 205 Pb dating in early Solar System

Radioactive nuclei with lifetimes on the order of millions of years can reveal the formation history of the Sun and active nucleosynthesis occurring at the time and place of its birth. Among such nuclei whose decay signatures are found in the oldest meteorites, 205 Pb is a powerful example, as it is produced exclusively by slow neutron captures (the s process), with most being synthesized in asymptotic giant branch (AGB) stars. However, making accurate abundance predictions for 205 Pb has so far been impossible because the weak decay rates of 205 Pb and 205 Tl are very uncertain at stellar temperatures. To constrain these decay rates, we measured for the first time the bound-state β - decay of fully ionized 205 Tl 81+ , an exotic decay mode that only occurs in highly charged ions. The measured half-life is 4.7 times longer than the previous theoretical estimate and our 10% experimental uncertainty has eliminated the main nuclear-physics limitation. With new, experimentally backed decay rates, we used AGB stellar models to calculate 205 Pb yields. Propagating those yields with basic galactic chemical evolution (GCE) and comparing with the 205 Pb/ 204 Pb ratio from meteorites, we determined the isolation time of solar material inside its parent molecular cloud. We find positive isolation times that are consistent with the other s-process short-lived radioactive nuclei found in the early Solar System. Our results reaffirm the site of the Sun’s birth as a long-lived, giant molecular cloud and support the use of the 205 Pb– 205 Tl decay system as a chronometer in the early Solar System.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Emerging supersolidity in photonic-crystal polariton condensates

A supersolid is a counter-intuitive phase of matter in which its constituent particles are arranged into a crystalline structure, yet they are free to flow without friction. This requires the particles to share a global macroscopic phase while being able to reduce their total energy by spontaneous, spatial self-organization. The existence of the supersolid phase of matter was speculated more than 50 years ago1, 2, 3–4. However, only recently has there been convincing experimental evidence, mainly using ultracold atomic Bose–Einstein condensates (BECs) coupled to electromagnetic fields. There, various guises of the supersolid were created using atoms coupled to high-finesse cavities5,6, with large magnetic dipole moments7, 8, 9, 10, 11, 12–13, and spin–orbit-coupled, two-component systems showing stripe phases14, 15–16. Here we provide experimental evidence of a new implementation of the supersolid phase in a driven-dissipative, non-equilibrium context based on exciton–polaritons condensed in a topologically non-trivial, bound state in the continuum (BiC) with exceptionally low losses, realized in a photonic-crystal waveguide. We measure the density modulation of the polaritonic state indicating the breaking of translational symmetry with a precision of several parts in a thousand. Direct access to the phase of the wavefunction allows us to also measure the local coherence of the supersolid. We demonstrate the potential of our synthetic photonic material to host phonon dynamics and a multimode excitation spectrum.

Trypogeorgos, Dimitrios↗
DOE OSTI2022

Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception

KAI2 proteins are plant α/β hydrolase receptors which perceive smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). The number of functional KAI2 receptors varies among species and KAI2 gene duplication and sub-functionalization likely plays an adaptative role by altering specificity towards different KLs. Legumes represent one of the largest families of flowering plants and contain many agronomic crops. Prior to their diversification, KAI2 underwent duplication resulting in KAI2A and KAI2B. Here we demonstrate that Pisum sativum KAI2A and KAI2B are active receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a higher affinity for and hydrolyses a broader range of substrates including strigolactone-like stereoisomers. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical, structural, and mass spectra analyses of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, confirming its role as a bona fide enzyme. Our work uncovers the stereoselectivity of ligand perception and catalysis by diverged KAI2 receptors and proposes adaptive sensitivity to KAR/KL and strigolactones by KAI2B.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir

We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K dimer , catalytic efficiency, and inhibitor binding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Coupled electronic and magnetic excitations in the cuprates and their role in the superconducting transition

The formation of Cooper pairs, a bound state of two electrons of opposite spin and momenta by exchange of a phonon, is a defining feature of conventional superconductivity. In the cuprate high temperature superconductors, even though the superconducting state also consists of Cooper pairs, the pairing mechanism remains intensely debated. Here, we investigate superconducting pairing in the Bi 2 Sr 2 CaCu 2 O 8+δ (Bi2212) cuprate by employing spectral functions obtained from angle-resolved photoemission as input to the Bethe-Salpeter equation. Assuming Cooper pairing is driven by spin fluctuations, we construct the spin-fluctuation-mediated pairing interaction and use it to compute the eigenfunctions and eigenvalues of the Bethe-Salpeter equation for multiple Bi2212 samples. The leading d-wave eigenvalue increases as the temperature is decreased toward $T_c$, reaching a value of approximately 1 at the $T_c$ corresponding to each doping value. This suggests that spin fluctuations can approximately account for $T_c$ and mediate pairing in the cuprate superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗