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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase

Abstract Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2′-deoxy-2′-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Initially Disordered, Reflectin Assembly Tunably and Reversibly Drives Biophotonic Color

Reflectin proteins are found in the reflective Bragg lamellae in skin cells of certain squids, where they tunably control color for camouflage and communication. Initially disordered in the monomeric form, the reflectins have unusual amino acid compositions and are block copolymers consisting of polyampholytic canonical repeats interspersed with cationic linkers. In vivo, phosphorylation of the cationic linkers induces condensation, secondary folding and hierarchical assembly of the reflectins with concomitant emergence of tunable iridescence. We analyzed the folding and assembly of recombinant phospho‐mimetic and deletion mutants of reflectin, using pH titration as a surrogate for in vivo phosphorylation. Results of dynamic light scattering, transmission electron microscopy, fluorescence, circular dichroism and x‐ray scattering reveal that neutralization of the cationic linkers progressively and reversibly drives the reflectins to form monodisperse spherical assemblies of reproducible size. These analyses reveal a strongly predictive relationship between net charge density and size of the assembled reflectin multimers, with the switch appearing to be equally distributed across the spatially segregated linkers. Accompanying the progressive neutralization of Coulombic repulsion of the linkers, assembly appears to be driven by entropically driven folding of the canonical repeats into amphiphilic secondary structures that are likely to enable hierarchical assembly. These results suggest a model for tunable reflectin assembly and provide insight into the behavior of this unique, initially disordered protein. Support or Funding Information This research was supported by the U.S. Department of Energy, U.S. Army Research Office, and Institute of Collaborative Biotechnologies. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Levenson, Robert↗
DOE OSTI2025

Linear magnetoconductivity as a probe of time-reversal symmetry breaking

Several optical experiments have shown that in magnetic materials, the principal axes of response tensors can rotate as an odd function of an applied magnetic field. Here we offer a microscopic explanation of this effect, and we propose a closely related dc transport phenomenon—an off-diagonal symmetric conductivity, linear and odd in a magnetic field, which we refer to as linear magnetoconductivity (LMC). Although LMC has the same functional dependence on a magnetic field as the Hall effect, its origin is fundamentally different: LMC requires time-reversal symmetry to be broken even before a magnetic field is applied, and is therefore a sensitive probe of magnetism. We demonstrate LMC in three different ways: via a tight-binding toy model, a density functional theory calculation on MnPSe3, and a semiclassical treatment. The third approach identifies two distinct mechanisms yielding LMC: momentum-dependent band magnetization and Berry curvature. Finally, we propose an experimental geometry suitable for detecting LMC, and we demonstrate its applicability using Landauer-Büttiker simulations. Our results emphasize the importance of measuring the full conductivity tensor in magnetic materials, and they introduce LMC as a new transport probe of symmetry.

Sunko, V↗
DOE OSTI2026

Nanoscale Defects as Probes of Time-Reversal Symmetry Breaking

Nanoscale defects such as nitrogen-vacancy (NV) centers can serve as sensitive and noninvasive probes of electromagnetic fields and fluctuations from materials, which in turn can be used to characterize these systems. Here we specifically discuss how NV centers can probe time-reversal symmetry breaking (TRSB) phenomena in low-dimensional electronic systems. We argue that the difference in relaxation rates Γ$_{±\hat{z}}$ of NV centers starting from 𝑚 = ±1 spin states to the ground state with 𝑚 = 0 directly probes TRSB. The effect arises from the difference in the fluctuation spectrum of left- and right-polarized electromagnetic fields emanating from such materials. In the quantum Hall setting, the NV center experiences (nearly zero) large additional contribution to its relaxation due to the presence of the material when its magnetic dipole (anti)aligns with the external field. More generally, the difference in the relaxation rates is sensitive to the imaginary part of the wave-vector-dependent Hall conductivity. We argue that this can be used to determine the Hall viscosity, which can potentially distinguish candidate fractional quantum Hall states and be used to infer the pairing angular momentum in TRSB superconductors. We compute the average relaxation rate [Γ$_{+\hat{z}}$ + Γ$_{-\hat{z}}$] near thin film superconductors and find that it exhibits a Hebel-Slichter-like enhancement below 𝑇 𝑐 . The difference Γ$_{+\hat{z}}$ −Γ$_{-\hat{z}}$ also inherits this peak but is only nonzero for 𝑇 < 𝑇 𝑐 and only if the superconductivity is chiral. We provide concrete estimates for observing this effect in stacked twisted bismuth strontium calcium copper oxide flakes.

NV centers↗
DOE OSTI2026

Indirect tunneling enabled spontaneous time-reversal symmetry breaking and Josephson diode effect in TiN/Al 2 ⁢O 3 /Hf 0.8 ⁢Zr 0.2 ⁢O 2 /Nb tunnel junctions

Josephson diode (JD) effect in Josephson tunnel junctions (JTJs) has attracted a great deal of attention due to its importance for developing superconducting-circuitry-based quantum technologies. Even though the preparation of high-quality JTJs by techniques employed in the semiconductor industry has been demonstrated, which was an important milestone because JTJs are the building blocks of superconducting electronics even before the quantum era, the JD effect has not been accomplished in them, nor has the highly desirable electrical control of the effect. We report here the fabrication of JTJs featuring a composite tunnel barrier of Al 2 ⁢O 3 and Hf 0.8 ⁢Zr 0.2 ⁢O 2 using complementary-metal-oxide-semiconductor compatible atomic layer deposition. These JTJs were found to show the JD effect in nominally zero magnetic fields with nonreciprocity controllable via an electric training current, yielding a surprisingly large diode efficiency. The quasiparticle tunneling, through which the Josephson coupling in a JTJ is established, was found to show theoretically expected gap features but no nonreciprocity. We attribute these observations to the simultaneous presence of positive and negative local Josephson couplings in the JTJs, with the negative Josephson coupling originating from indirect tunneling, which results in spontaneous time-reversal symmetry breaking. Finally, the double-minima washboard potential for the ensemble-averaged phase difference in the resistively and capacitively shunted junction model is shown to fully account for the experimentally observed JD effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Spontaneous magnon decays from nonrelativistic time-reversal symmetry breaking in altermagnets

Quasiparticles are central to condensed matter physics, but their stability can be undermined by quantum many-body interactions. Magnons, i.e., quasiparticles in quantum magnets, are particularly intriguing because their properties are governed by both real and spin space. While crystal symmetries may be low, spin interactions often remain approximately isotropic, limiting spontaneous magnon decay. Textbook wisdom holds that collinear Heisenberg magnets follow a dichotomy: ferromagnets host stable magnons, while antiferromagnetic magnons may decay depending on dispersion curvature. Up to now, relativistic spin-orbit coupling and noncollinear order that connect spin space to real space were shown to introduce more complex magnon instability mechanisms. Here, we show that even in nonrelativistic isotropic collinear systems, this conventional dichotomy is disrupted in altermagnets. Altermagnets, a newly identified class of collinear magnets, exhibit compensated spin order with nonrelativistic time-reversal symmetry breaking and even-parity band splitting. Using kinematic analysis, nonlinear spin-wave theory, and quantum simulations, we reveal that even weak band splitting opens a decay phase space, driving quasiparticle breakdown. Additionally, 𝑑-wave altermagnets form a rare “island of stability” at the Brillouin-zone center. Furthermore, our findings establish a quasiparticle stability trichotomy in collinear Heisenberg magnets and position altermagnets as a promising platform for unconventional spin dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Origin and limit of the recovery of damaged information by time reversal

Recently it was found that scrambled information can be partially recovered by a time-reversed evolution, even after being damaged by an intruder. Here we reconsider the origin of the information recovery, and argue that the presence of classical chaos does not preclude it and only leads to a quantitative reduction of the recovery ratio. We also show how decoherence (i.e., entanglement with the intruder) limits the recovery, by proving an upper bound on the recovery ratio in terms of the entangling power of the intruder's action.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Energy Conversion from Heat to Electricity by Highly Reversible Phase-Transforming Ferroelectrics

The search for performant multiferroic materials has attracted general research interest in energy science as they have been increasingly exploited as the conversion media among thermal, electric, magnetic, and mechanical energies by using their temperature-dependent ferroic properties. Here we report a material development strategy that guides us to discover a reversible phase-transforming ferroelectric material exhibiting enduring energy harvesting from small temperature differences. The material satisfies the crystallographic compatibility condition between polar and nonpolar phases, which shows only 2.5°C thermal hysteresis and a high figure of merit. It stably generates 15μA of electricity in consecutive thermodynamic cycles in the absence of any bias fields. We demonstrate our device to consistently generate 6μA/cm 2 current density near 100°C over 540 complete phase transformation cycles without any electric and functional degradation. The energy-conversion device can light up an LED directly without attaching an external power source. Furthermore, this promising material candidate brings the low-grade waste-heat harvesting closer to a practical realization, e.g., small temperature fluctuations around the water boiling point can be considered as a clean energy source.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2021

Effect of Surface Ionic Screening on Polarization Reversal and Phase Diagrams in Thin Antiferroelectric Films for Information and Energy Storage

Emergent behaviors in antiferroelectric thin films due to a coupling between surface electrochemistry and intrinsic polar instabilities are explored within the framework of the modified 2-4-6 Landau-Ginzburg-Devonshire (LGD) thermodynamic approach. By using phenomenological parameters of the LGD potential for a bulk antiferroelectric and a Stephenson-Highland (SH) approach, we study the role of surface ions with a charge density proportional to the relative partial oxygen pressure on the dipole states and their reversal mechanisms in antiferroelectric thin films. The combined LGDSH approach allows the boundaries of antiferroelectric, ferroelectriclike antiferroionic, and electretlike paraelectric states as a function of temperature, oxygen pressure, surface-ion formation energy and concentration, and film thickness to be delineated. This approach also allows the characterization of the polar and antipolar orderings dependence on the voltage applied to the antiferroelectric film, as well as the analysis of their static and dynamic hysteresis loops. Furthermore, the applications of the antiferroelectric films covered with a surface-ion layer for energy and information storage are explored and discussed.

25 ENERGY STORAGE↗
DOE OSTI2020

Time-reversal invariant and fully gapped unconventional superconducting state in the bulk of the topological compound Nb 0.25 Bi 2 Se 3

Recently, the niobium (Nb) doped topological insulator Bi 2 Se 3 , in which the finite magnetic moments of the Nb atoms are intercalated in the van der Waals gap between the Bi 2 Se 3 layers, has been shown to exhibit both superconductivity with $T_c$ ≃ 3 K and topological surface states. Here we report on muon spin rotation experiments probing the temperature and field dependence of effective magnetic penetration depth $λ_{\text{eff}}(T)$ in the layered topological superconductor candidate Nb 0.25 Bi 2 Se 3 . In this work the exponential temperature dependence of $λ^{–2}_{\text{eff}}(T)$ at low temperatures suggests a fully gapped superconducting state in the bulk with the superconducting transition temperature $T_c$ = 2.9 K and the gap to $T_c$ ratio 2Δ /$k_BT_c$ = 3.95(19). We also reveal that the ratio Tc/λ–2eff is comparable to those of unconventional superconductors, which hints at an unconventional pairing mechanism. Furthermore, time-reversal symmetry breaking was excluded in the superconducting state with sensitive zero-field μSR experiments. We hope the present results will stimulate theoretical investigations to obtain a microscopic understanding of the relation between superconductivity and the topologically nontrivial electronic structure of Nb 0.25 Bi 2 Se 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Reversible ratchet effects in a narrow superconducting ring

We study the ratchet effect in a narrow pinning-free superconductive ring based on time-dependent GinzburgLandau (TDGL) equations. Voltage responses to external dc and ac currents at various magnetic fields are studied. Due to asymmetric barriers for flux penetration and flux exit in the ring-shaped superconductor, the critical current above which the flux-flow state is reached, as well as the critical current for the transition to the normal state, are different for the two directions of applied current. Furthermore, these effects cooperatively cause ratchet signal reversal at high magnetic fields, which has not been reported to date in a pinning-free system. The ratchet signal found here is larger than those induced by asymmetric pinning potentials. Our results also demonstrate the feasibility of using mesoscopic superconductors to employ a superconducting diode effect in versatile superconducting devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Determination of rutile transition metal oxide (110) surface terminations by scanning tunneling microscopy contrast reversal

The surfaces of rutile transition-metal oxides (TMO 2 ) are widely investigated for catalysis, photoelectrochemical solar cells, memristors, and supercapacitors, but their structures have remained controversial. Here we employ density functional theory to predict that a universal behavior of metallic TMO 2 surfaces, i.e., the stoichiometric TMO 2 surfaces, exhibit a contrast reversal in simulated scanning tunneling microscopy (STM) images at different scanning biases. The predictions are verified by experimental STM imaging of RuO 2 (110) surfaces and this feature is shown to enable accurate determinations of the TMO 2 (110) surface structures under various conditions. This research provides different insights into the electronic properties of TMO 2 (110) surfaces and offers an effective method to directly map the surface structure and point defects using bias-dependent STM.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Dynamical piezomagnetic effect in time-reversal-invariant Weyl semimetals with axionic charge density waves

Charge density waves (CDWs) in Weyl semimetals (WSMs) have been shown to induce an exotic axionic insulating phase in which the sliding mode (phason) of the CDW acts as a dynamical axion field, giving rise to a large positive magnetoconductance. In this work, we predict that dynamical strain can induce a bulk orbital magnetization in time-reversal (TR)-invariant WSMs that are gapped by a CDW. Here, we term this effect the “dynamical piezomagnetic effect” (DPME). Unlike in J. Gooth et al., the DPME introduced in this work occurs in a bulk-constant (i.e., static and spatially homogeneous in the bulk) CDW, and does not rely on fluctuations, such as a phason. By studying the low-energy effective theory and a minimal tight-binding (TB) model, we find that the DPME originates from an effective valley axion field that couples the electromagnetic gauge field with a strain-induced pseudogauge field. In particular, whereas the piezoelectric effects studied in previous works are characterized by 2D Berry curvature, the DPME represents the first example of a fundamentally 3D strain effect originating from the Chern-Simons 3-form. We further find that the DPME has a discontinuous change at a critical value of the phase of the CDW order parameter. We demonstrate that, when there is a jump in the DPME, the surface of the system undergoes a topological quantum phase transition (TQPT), while the bulk remains gapped. Hence, the DPME provides a bulk signature of the boundary TQPT in a TR-invariant Weyl CDW.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Reversible motions and disordered structure of soft particles in amorphous solids

In amorphous solids, soft vibrational modes derived from normal mode analysis can be utilized to identify the soft particles that are prone to irreversible rearrangements. However, the normal mode analysis approach cannot explain why the spatial distributions of clustered soft particles do not change over time. We define a softness parameter based on the vibrational density of states calculated directly from molecular dynamics simulations with both the harmonic vibrations and anharmonic relaxations being properly captured at finite temperatures. This parameter spontaneously correlates with the real space atomic motions and the dynamics heterogeneity. Using the softness parameter, we show that the softest particles are confined within rigid cages. These particles keep rearranging reversibly without long-range diffusion. The moderately soft particles rearrange irreversibly, and the hard particles mainly participate in vibrations without rearrangement. Here, we also show that the soft particles form locally disordered structures, while the hard particles present strong ordering. These findings confirm the defective nature of soft particles, and provide insights on the nature of softness as the ability to rearrange, but not necessarily irreversibly.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Nanomagnet shape effects on magnetic reversal in artificial spin ice

We use micromagnetic simulations to study the influence of the shape of elongated nanomagnets that vary from rectangular to elliptical shapes in an artificial spin ice array. For weakly interacting ellipselike islands, the magnetic hysteresis loops align with the Stoner-Wohlfarth model, demonstrating nearly uniform magnetization at remanence and nearly coherent rotation. As expected, nonelliptical weakly interacting islands show deviations from the model due to the curling and pinning of the magnetization at the island edge. We find that increasing interisland coupling leads to an increasingly complex magnetic reversal process due to an interplay between internal and external degrees of freedom as the shape of the islands varies. Furthermore, our results open a roadmap for tailoring systems with desired magnetic properties by choosing the appropriate nanomagnet shape.

Artificial spin ice↗
DOE OSTI2015

Toward reversing Joule heating with a phonon-absorbing heterobarrier

Using a graded heterobarrier placed along an electron channel, phonons emitted in Joule heating are recycled in situ by increasing the entropy of phonon-absorbing electrons. The asymmetric electric potential distribution created by alloy grading separates the phonon absorption and emission regions, and emission in the larger effective-mass region causes momentum relaxation with smaller electron kinetic energy loss. These lead to smaller overall phonon emission and simultaneous potential-gain and self-cooling effects. Larger potential is gained with lower current and higher optical-phonon temperature. The self-consistent Monte Carlo simulations complying with the lateral momentum conservation combined with the entropy analysis are applied to a GaAs:Al electron channel with a graded heterobarrier, and under ideal lateral thermal isolation from surroundings, the phonon recycling efficiency reaches 25% of the reversible limit at 350 K, and it increases with temperature. In conclusion, the lateral momentum contributes to the transmission across the barrier, so partially nonconserving lateral momentum electron scattering (rough interface) can improve efficiency.

42 ENGINEERING↗
DOE OSTI2016

Atomic structure of Pt nanoclusters supported by graphene/Ir(111) and reversible transformation under CO exposure

We investigate the atomic structure of graphene/Ir(111) supported platinum clusters with on average fewer than 40 atoms by means of surface x-ray diffraction (SXRD), grazing incidence small angle x-ray scattering (GISAXS), and normal incidence x-ray standing waves (NIXSW) measurements, in comparison with density functional theory calculations (DFT). GISAXS revealed that the clusters with 1.3 nm diameter form a regular array with domain sizes of 90 nm. SXRD shows that the 1–2 monolayer high, (111) oriented Pt nanoparticles grow epitaxially on the graphene support. From the combined analysis of the SXRD and NIXSW data, a three-dimensional (3D) structural model of the clusters and the graphene support can be deduced which is in line with the DFT results. For the clusters grown in ultrahigh vacuum the lattice parameter is reduced by (4.6±0.1)% compared to bulk platinum. The graphene layer undergoes a strong Pt adsorption induced buckling, caused by a rehybridization of the carbon atoms below the cluster. Lastly, in situ observation of the Pt clusters in CO and O 2 environments revealed a reversible change of the clusters' strain state while successively dosing CO at room temperature and O 2 at 575 K, pointing to a CO oxidation activity of the Pt clusters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

First-order reversal curve of the magnetostructural phase transition in FeTe

We apply the first-order reversal curve (FORC) method, adapted from studies of ferromagnetic materials, to the magnetostructural phase transition of Fe 1+y Te. FORC measurements reveal two features in the hysteretic phase transition, even in samples where traditional temperature measurements display only a single transition. For Fe 1.13 Te, the influence of magnetic field suggests that the main feature is primarily structural while a smaller, slightly higher-temperature transition is magnetic in origin. By contrast, Fe 1.03 Te has a single transition which shows a uniform response to magnetic field, indicating a stronger coupling of the magnetic and structural phase transitions. We also introduce uniaxial stress, which spreads the distribution width without changing the underlying energy barrier of the transformation. Finally, the work shows how FORC can help disentangle the roles of the magnetic and structural phase transitions in FeTe.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗