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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Revealing the frequency-dependent oscillations in the nonlinear terahertz response induced by the Josephson current

ABSTRACT Nonlinear responses of superconductors to intense terahertz radiation has been an active research frontier. Using terahertz pump-terahertz probe spectroscopy, we investigate the c-axis nonlinear optical response of a high-temperature superconducting cuprate. After excitation by a single-cycle terahertz pump pulse, the reflectivity of the probe pulse oscillates as the pump-probe delay is varied. Interestingly, the oscillatory central frequency scales linearly with the probe frequency, a fact widely overlooked in pump-probe experiments. By theoretically solving the nonlinear optical reflection problem on the interface, we show that our observation is well explained by the Josephson-type third-order nonlinear electrodynamics, together with the emission coefficient from inside the material into free space. The latter results in a strong enhancement of the emitted signal whose physical frequency is around the Josephson plasma edge. Our result offers a benchmark for and new insights into strong-field terahertz spectroscopy of related quantum materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Late day measurement of excised branches results in uncertainty in the estimation of two stomatal parameters derived from response curves in Populus deltoides Bartr. x Populus nigra L.

Many terrestrial biosphere models depend on an understanding of the relationship between stomatal conductance and photosynthesis. However, unlike the measurement of photosynthetic parameters, such as the maximum carboxylation capacity, where standard methods (e.g., CO 2 response or ACi curves) are widely accepted, a consensus method for empirically measuring parameters representing stomatal response has not yet emerged. Most models of stomatal response to environment represent stomatal conductance as being bounded by a lower intercept parameter (g 0 ), and linearly scaled based on a multivariate term described by the stomatal slope parameter (g 1 ). Here we employ the widely used Unified Stomatal Optimization model, to test whether g 1 and g 0 parameters are impacted by the choice of measurement method, either on an intact branch, or a cut branch segment stored in water. We measured paired stomatal response curves on intact and excised branches of a hybrid poplar clone (Populus deltoides Bartr. x Populus nigra L. OP367), measured twice over a diurnal period. We found that predawn branch excision did not significantly affect measured g 0 and g 1 when measured within 4 h of excision. Measurement in the afternoon resulted in significantly higher values of g 1 and lower values of g0, with values changing by 55% and 56% respectively. Excision combined with afternoon measurement resulted in a marked effect on parameter estimates, with g1 increasing 89% from morning to afternoon and a 25% lower g 1 for cut branches than those measured in situ. We also show that in hybrid poplar the differences in parameter estimates obtained from plants measured under different conditions can directly impact models of canopy function, reducing modeled transpiration by 18% over a simulated 12.5-hour period. While these findings are only for a single isohydric woody species, our findings suggest that stomatal optimality parameters may not remain constant throughout the day.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Development of a new quantum trajectory molecular dynamics framework

An extension to the wave packet description of quantum plasmas is presented, where the wave packet can be elongated in arbitrary directions. A generalized Ewald summation is constructed for the wave packet models accounting for long-range Coulomb interactions and fermionic effects are approximated by purpose-built Pauli potentials, self-consistent with the wave packets used. We demonstrate its numerical implementation with good parallel support and close to linear scaling in particle number, used for comparisons with the more common wave packet employing isotropic states. Ground state and thermal properties are compared between the models with differences occurring primarily in the electronic subsystem. Especially, the electrical conductivity of dense hydrogen is investigated where a 15% increase in DC conductivity can be seen in our wave packet model compared with other models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Influence of Markovianity and self-consistency on time-resolved spectral functions of driven quantum systems

We present a systematic comparison of the real-time Dyson expansion (RTDE) with established nonequilibrium Green's function (GF) approaches for simulating driven, interacting quantum systems. Focusing on density matrix dynamics, time-off-diagonal GFs, and time-resolved photoemission spectra, we benchmark RTDE against fully self-consistent Kadanoff-Baym equation (KBE) calculations, the generalized Kadanoff-Baym ansatz, and exact diagonalization for small systems using second-order many-body perturbation theory. Using a driven two-band Hubbard model, we show that mean-field single-particle density matrix trajectories provide a reliable baseline for RTDE across a broad range of interaction strengths and excited-carrier populations. Further, RTDE accurately captures correlation effects in the GFs, including long-lived oscillations and revivals that are strongly suppressed by the overdamping inherent to self-consistent KBE schemes. As a consequence, RTDE resolves rich nonequilibrium spectral structure in time-resolved photoemission, such as interaction- and population-dependent quasiparticle splittings and band gap renormalization, which are largely washed out in self-consistent approaches yet are present in exact solutions. Furthermore, our results demonstrate that RTDE bridges the gap between mean-field propagation and full two-time KBE simulations, retaining favorable linear scaling while capturing essential dynamical correlations relevant for ultrafast spectroscopy.

Electronic structure↗
DOE OSTI2026

Observation of a Goldstone mode in the broken helix by time-resolved optical polarimetry

Magnets with isotropic easy-plane symmetry host Goldstone modes that can be leveraged for efficient spin transport. Here, we present a time-resolved optical polarimetry technique that allows us to detect and characterize such low-frequency modes, and use it to observe the Goldstone mode in the multi-Q broken helix phase of EuIn2As2. The strength of our technique comes from the ability to distinguish between nematic and magnetization dynamics in order to yield information about the mode structure, in addition to its frequency. We find that the nearly uniform spin precession characteristic of a Goldstone mode is realized only when a small magnetic field is used to unpin the broken helix from local strain generated during crystal growth. In this regime, the mode frequency scales linearly with the applied field due to the ground state C2z symmetry of the broken helix. Our work shows how optical polarimetry can be used to study the Goldstone modes of complex magnets.

Liebman-Peláez, A↗
DOE OSTI2026

Simple algorithm for polarized parton evolution

We present an algorithm to include the correlation between the production and decay planes of gluons in a parton-shower simulation. The technique is based on identifying the charge currents responsible for the creation and annihilation of the vector field. It is applicable in both the hard-collinear and the soft wide-angle region. As a function of the number of particles, the algorithm scales linear in computing time and memory. We demonstrate agreement with fixed-order perturbative calculations in the relevant kinematical limits, and present a new observable that can be used to probe correlations beyond current-current interactions.

Höche, Stefan [Fermi National Accelerator Laborato↗
DOE OSTI2026

Faster Randomized Dynamical Decoupling

We present a randomized dynamical decoupling (DD) protocol that can substantially improve the performance of any given deterministic DD scheme for suppressing coherent noise by using no more than two additional pulses. Our construction is implemented by probabilistically applying sequences of pulses, which, when combined, effectively eliminate the error terms that scale linearly with the system-environment coupling strength. As a result, we show that a randomized protocol using a few pulses can outperform deterministic DD protocols that require considerably more pulses. Furthermore, we prove that the randomized protocol provides an improvement compared to deterministic DD sequences that aim to reduce the error in the system’s Hilbert space, such as Uhrig DD, which had been previously regarded to be optimal. To rigorously evaluate the performance, we introduce new analytical methods suitable for analyzing higher-order DD protocols that might be of independent interest. Here, we also present numerical simulations confirming the significant advantage of using randomized protocols compared to widely used deterministic protocols.

Quantum algorithms & computation↗
DOE OSTI2024

Stochastic Maxwell-Bloch equations for modeling amplified spontaneous emission

An approach for studying atom-radiation interaction has been developed, associating quantum operators with stochastic variables governed by discrete Heisenberg equations. This framework models general multilevel atomic systems using the paraxial approximation in both single- and multipass configurations. Simulation results for x-ray laser oscillators with parameters of interest are presented. Finally, the stochastic model is efficient to solve, as the required computational resources scale linearly with the number of emitters, and it may be applicable to various other quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Relaxation of the degenerate one-dimensional Fermi gas

In this work, we study how a system of one-dimensional spin-1/2 fermions at temperatures well below the Fermi energy approaches thermal equilibrium. The interactions between fermions are assumed to be weak and are accounted for within the perturbation theory. In the absence of an external magnetic field, spin degeneracy strongly affects relaxation of the Fermi gas. For sufficiently short-range interactions, the rate of relaxation scales linearly with temperature. Focusing on the case of the system near equilibrium, we linearize the collision integral and find the exact solution of the resulting relaxation problem. Furthermore, we discuss the application of our results to the evaluation of the transport coefficients of the one-dimensional Fermi gas.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Majorana-based quantum computing in nanowire devices

The boundary of one-dimensional topological superconductors might lead to the appearance of Majorana zero modes, whose nontrivial exchange statistics can be used for quantum computing. In branched nanowire networks, one can exchange Majorana modes by time dependently tuning topologically nontrivial parameter regions. In this paper, we simulate the exchange of four Majorana modes in T-shaped junctions made out of $\textit{p}$-wave superconducting Rashba wires. Specifically, we derive concrete experimental predictions for (quasi-)adiabatic braiding times and determine geometric conditions for successful Majorana exchange processes. Moreover, we prove that, in the adiabatic limit, the gating time needs to be smaller than the inverse of the squared superconducting order parameter and scales linearly with the gating potential. Furthermore, we show how to circumvent the formation of additional Majorana modes in branched nanowire systems, arising at wire intersection points of narrow junctions. Finally, we propose a multiqubit setup, allowing for universal quantum computing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Anomalous Hall effect in the weak-itinerant ferrimagnet FeCr 2 Te 4

In this study, we carried out a comprehensive study of electronic transport, thermal, and thermodynamic properties in Fe Cr 2 Te 4 single crystals. It exhibits bad-metallic behavior and anomalous Hall effect (AHE) below a weak-itinerant paramagnetic-to-ferrimagnetic transition T c ~ 123 K. The linear scaling between the anomalous Hall resistivity ρ x y and the longitudinal resistivity ρ x x implies that the AHE in Fe Cr 2 Te 4 is most likely dominated by an extrinsic skew-scattering mechanism rather than an intrinsic KL or an extrinsic side-jump mechanism, which is supported by our Berry phase calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Magnetic anisotropy and spin dynamics in the kagome magnet Fe 4 Si 2 Sn 7 O 16 : NMR and magnetic susceptibility study on oriented powder

Fe 4 Si 2 Sn 7 O 16 hosts an undistorted kagome lattice of Fe 2+ (3d 6 , S = 2) ions. We present results of bulk magnetization and Sn nuclear magnetic resonance (NMR) measurements on an oriented Fe 4 Si 2 Sn 7 O 16 powder sample oriented in geometries parallel (∥) and perpendicular (⊥) to the external applied magnetic field used for orienting the powder (Bori). The bulk susceptibility χ shows a broad peak at T N ~ 3 K associated with antiferromagnetic ordering. NMR spectra indicate the presence of planar anisotropy in the kagome planes. From an analysis of the static NMR shift (K) and dynamic spin-lattice relaxation rate (1/T 1 ) we conclude the presence of dominant magnetic fluctuations in the kagome planes. For the ∥ orientation, K scales linearly with the bulk susceptibility for temperatures down to ~ 4 K, while in the ⊥ orientation K starts to deviate strongly below T ~ 30 K. We associate this deviation with the onset of spin-tilting towards the kagome planes. These correlations are also reflected in the 1/T 1 data for the ∥ orientation, which starts to decrease below T ~ 30 K. Here, in this correlated regime, T N < T < ~ 30 K, we discuss the formation of positive chiral spin correlations in the kagome planes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Local atomic and magnetic structure of multiferroic (Sr,Ba)⁢(Mn,Ti)⁢O 3

Here, we present a detailed study of the local atomic and magnetic structure of the type-I multiferroic perovskite system (Sr,Ba)(Mn,Ti)O 3 using x-ray and neutron pair distribution function (PDF) analysis, polarized neutron scattering, and muon spin relaxation (μSR) techniques. The atomic PDF analysis reveals widespread nanoscale tetragonal distortions of the crystal structure even in the paraelectric phase with average cubic symmetry, corresponding to incipient ferroelectricity in the local structure. Magnetic PDF analysis, polarized neutron scattering, and μSR likewise confirm the presence of short-range antiferromagnetic correlations in the paramagnetic state, which grow in magnitude as the temperature approaches the magnetic transition. We show that these short-range magnetic correlations coincide with a reduction of the tetragonal (i.e., ferroelectric) distortion in the average structure, suggesting that short-range magnetism can play an important role in magnetoelectric and/or magnetostructural phenomena even without genuine long-range magnetic order. The reduction of the tetragonal distortion scales linearly with the local magnetic order parameter, pointing to spontaneous linear magnetoelectric coupling in this system. These findings provide greater insight into the multiferroic properties of (Sr,Ba)(Mn,Ti)O 3 and demonstrate the importance of investigating the local atomic and magnetic structure to gain a deeper understanding of the intertwined degrees of freedom in multiferroics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Self-consistent quasiparticle G W and hybrid functional calculations for Al/InAs/Al heterojunctions: Band offset and spin-orbit coupling effects

The electronic structure of surfaces and interfaces plays a key role in the properties of quantum devices. Here, we study the electronic structure of realistic Al/InAs/Al heterojunctions using a combination of density functional theory with hybrid functionals and state-of-the-art quasiparticle G W (QSGW) calculations. We find a good agreement between QSGW calculations and hybrid functional calculations, which themselves compare favorably well with angle-resolved photoemission spectroscopy experiments. Our paper confirms the need for well-controlled quality of the interfaces to obtain the needed properties of InAs/Al heterojunctions. A detailed analysis of the effects of spin-orbit coupling on the spin splitting of the electronic states shows a linear scaling in k space, related to the two-dimensional nature of some interface states. The good agreement by QSGW and hybrid functional calculations opens the door towards trustable use of an effective approximation to QSGW for studying very large heterojunctions. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗
DOE OSTI2025

Low-energy edge signatures of the Kitaev spin liquid

Recent experimental work indicates that the Kitaev spin liquid may be realizable close to zero magnetic field in exfoliated 𝛼−RuCl 3 flakes, thus providing a more versatile setting for studying non-Abelian anyons. Here, we propose a robust nanoscale signature of the Kitaev spin liquid that results from its edge states and manifests in the low-energy spin dynamics. In particular, we highlight a singular peak in the dynamical spin structure factor of a zigzag edge whose energy scales linearly with only one component of the magnetic field. This sharp feature in the local spin dynamics directly reflects the bond-directional Kitaev spin interactions and, more generally, the projective symmetries of the Kitaev spin liquid. In conclusion, we demonstrate that our proposed signature survives in the presence of edge disorder as well as non-Kitaev interactions, and provide detailed guidelines for experimentally observing it using inelastic electron tunneling spectroscopy and color-center relaxometry.

Color centers↗
DOE OSTI2020

Generalized Kompaneets formalism for inelastic neutrino-nucleon scattering in supernova simulations

Based on the Kompaneets approximation, we develop a robust methodology to calculate spectral redistribution via inelastic neutrino-nucleon scattering in the context of core-collapse supernova simulations. The resulting equations conserve lepton number to machine precision and scale linearly, not quadratically, with number of energy groups. The formalism also provides an elegant means to derive the rate of energy transfer to matter which, as it must, automatically goes to zero when the neutrino radiation field is in thermal equilibrium. Furthermore, we derive the next higher order in $ϵ/mc^2$ correction to the neutrino Kompaneets equation. Unlike other Kompaneets schema, ours also generalizes to the case of anisotropic angular distributions, while retaining the conservative form that is a hallmark of the classical Kompaneets equation. In this work, our formalism enables immediate incorporation into supernova codes that follow the spectral angular moments of the neutrino radiation fields.

79 ASTRONOMY AND ASTROPHYSICS↗