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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 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparison of state-interaction and spinor-representation calculations of spin-orbit coupling within exact two-component coupled-cluster theories

Here a benchmark study of state-interaction and spinor-representation calculations of spin-orbit coupling using the exact two-component Hamiltonians with atomic mean-field integrals (the X2CAMF schemes) at the equation-of-motion coupled-cluster singles and doubles level is reported. We adopt a version of the X2CAMF scheme with spin-orbit integrals correct to first order for the state-interaction calculations and a version correct to infinite order for the spinor-representation calculations. The differences between the state-interaction calculations with minimum active spaces to account for (quasi-)degeneracy and the spinor-representation calculations thus correspond to higher-order spin-orbit contributions. This state-interaction approach with scalar-relativistic effects accurately included in the reference functions and in the spin-orbit integrals is shown to exhibit robust performance for elements across the periodic table. On the other hand, the more rigorous spinor representation shows more rapid convergence with respect to the number of correlated electrons and is the preferred choice for accurate calculations for heavy elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Neutrino(antineutrino)–nucleus interactions in the shallow- and deep-inelastic scattering regions

In $\nu /\bar{\nu }$–nucleon/nucleus interactions shallow inelastic scattering ($\text{SIS}$) is technically defined in terms of the four-momentum transfer to the hadronic system as non-resonant meson production with $Q^2 \lessapprox 1 \text {GeV}^2$. This non-resonant meson production intermixes with resonant meson production in a regime of similar effective hadronic mass W of the interaction. As $Q^2$ grows and surpasses this $ ≈1 \text{GeV}^2$ limit, non-resonant interactions begin to take place with quarks within the nucleon indicating the start of deep inelastic scattering ($\text{DIS}$). To essentially separate this resonant plus non-resonant meson production from $\text{DIS}$ quark-fragmented meson production, a cut of 2 $\text{GeV}$ in W of the interactions is generally introduced. However, since experimentally mesons from resonance decay cannot be separated from non-resonant produced mesons, $\text{SIS}$ for all practical purposes in this review has been defined as inclusive meson production that includes non-resonant plus resonant meson production and the interference between them. Experimentally then for $W \lessapprox 2 \text{GeV}$ inclusive meson production with $W \gtrapprox (M_N + M_π)$ and all $Q^2$ is here defined as $\text{SIS}$, while for $W \gtrapprox 2 \text {GeV}$, the kinematic region with $Q^2 \gtrapprox 1 \text{GeV}^2$ is defined as DIS$\text{DIS}$degrees of attention from the community. While the theoretical/phenomenological study of $\nu$–nucleon and $\nu$–nucleus $\text{DIS}$ scattering is advanced, such studies of a large portion of the $\text{SIS}$ region, particularly the $\text{SIS}$ to $\text{DIS}$ transition region, have hardly begun. Experimentally, the $\text{SIS}$ and the $\text{DIS}$ regions for $\nu$–nucleon scattering have minimal results and only in the experimental study of the $\nu$–nucleus $\text{DIS}$ region are there significant results for some nuclei. Inasmuch as current and future neutrino oscillation experiments have contributions from both higher $W \text{SIS}$ and $\text{DIS}$ kinematic regions and these regions are in need of both considerable theoretical and experimental study, this review will concentrate on these $\text{SIS}$ to $\text{DIS}$ transition and $\text{DIS}$ kinematic regions surveying our knowledge and the current challenges.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Skyrmion–skyrmion interaction in a magnetic film

Interaction of two skyrmions stabilized by the ferromagnetic exchange, Dzyaloshinskii–Moriya interaction (DMI), and external magnetic field has been studied numerically on a 2D lattice of size large compared to the separation, d, between the skyrmions. We show that two skyrmions of the same chirality (determined by the symmetry of the crystal) repel. In accordance with earlier analytical results, their long-range pair interaction falls out with the separation as exp(-d/δ H ), where δ H is the magnetic screening length, independent of the DMI. The prefactor in this expression depends on the DMI that drives the repulsion. The latter results in the spiral motion of the two skyrmions around each other, with the separation between them growing logarithmically with time. When two skyrmions of the total topological charge Q = 2 are pushed close to each other, the discreteness of the atomic lattice makes them collapse into one skyrmion of charge Q = 1 below a critical separation. Experiment is proposed that would allow one to measure the interaction between two skyrmions by holding them in positions with two magnetic tips. Our findings should be of value for designing topologically protected magnetic memory based upon skyrmions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

The effect of metal–insulator interface interactions on electrical transport in granular metals

Here, we present an in-depth study of metal–insulator interfaces within granular metal (GM) films and correlate their interfacial interactions with structural and electrical transport properties. Nominally 100 nm thick GM films of Co and Mo dispersed within yttria-stabilized zirconia (YSZ), with volumetric metal fractions (φ) from 0.2–0.8, were grown by radio frequency co-sputtering from individual metal and YSZ targets. Scanning transmission electron microscopy and DC transport measurements find that the resulting metal islands are well-defined with 1.7–2.6 nm average diameters and percolation thresholds between φ = 0.4–0.5. The room temperature conductivities for the φ = 0.2 samples are several orders of magnitude larger than previously-reported for GMs. X-ray photoemission spectroscopy indicates both oxygen vacancy formation within the YSZ and band-bending at metal–insulator interfaces. The higher-than-predicted conductivity is largely attributed to these interface interactions. In agreement with recent theory, interactions that reduce the change in conductivity across the metal–insulator interface are seen to prevent sharp conductivity drops when the metal concentration decreases below the percolation threshold. These interface interactions help interpret the broad range of conductivities reported throughout the literature and can be used to tune the conductivities of future GMs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Full configuration interaction simulations of exchange-coupled donors in silicon using multi-valley effective mass theory

Abstract Donor spins in silicon have achieved record values of coherence times and single-qubit gate fidelities. The next stage of development involves demonstrating high-fidelity two-qubit logic gates, where the most natural coupling is the exchange interaction. To aid the efficient design of scalable donor-based quantum processors, we model the two-electron wave function using a full configuration interaction method within a multi-valley effective mass theory. We exploit the high computational efficiency of our code to investigate the exchange interaction, valley population, and electron densities for two phosphorus donors in a wide range of lattice positions, orientations, and as a function of applied electric fields. The outcomes are visualized with interactive images where donor positions can be swept while watching the valley and orbital components evolve accordingly. Our results provide a physically intuitive and quantitatively accurate understanding of the placement and tuning criteria necessary to achieve high-fidelity two-qubit gates with donors in silicon.

Joecker, Benjamin (ORCID:0000000302635440)↗
DOE OSTI2020

Interacting radiation after Planck and its implications for the Hubble tension

Standard cosmology predicts that prior to matter-radiation equality about 41% of the energy density was in free-streaming neutrinos. In many beyond Standard Model scenarios, however, the amount and free-streaming nature of this component is modified. For example, this occurs in models with new neutrino self-interactions or an additional dark sector with interacting light particles. Here, we consider several extensions of the standard cosmology that include a non-free-streaming radiation component as motivated by such particle physics models and use the final Planck data release to constrain them. This release contains significant improvements in the polarization likelihood which plays an important role in distinguishing free-streaming from interacting radiation species. Fixing the total amount of energy in radiation to match the expectation from standard neutrino decoupling we find that the fraction of free-streaming radiation must be ffs > 0.8 at 95% CL (combining temperature, polarization and baryon acoustic oscillation data). Allowing for arbitrary contributions of free-streaming and interacting radiation, the effective number of new non-free-streaming degrees of freedom is constrained to be Nfld < 0.6 at 95% CL. Cosmologies with additional radiation are also known to ease the discrepancy between the local measurement and CMB inference of the current expansion rate H0. We show that including a non-free-streaming radiation component allows for a larger amount of total energy density in radiation, leading to a mild improvement of the fit to cosmological data compared to previously discussed models with only a free-streaming component.

particle physics - cosmology connection↗
DOE OSTI2023

Galaxy Interactions in Filaments and Sheets: Effects of the Large-scale Structures Versus the Local Density

Abstract Major interactions are known to trigger star formation in galaxies and alter their color. We study the major interactions in filaments and sheets using SDSS data to understand the influence of large-scale environments on galaxy interactions. We identify the galaxies in filaments and sheets using the local dimension and also find the major pairs residing in these environments. The star formation rate (SFR) and color of the interacting galaxies as a function of pair separation are separately analyzed in filaments and sheets. The analysis is repeated for three volume limited samples covering different magnitude ranges. The major pairs residing in the filaments show a significantly higher SFR and bluer color than those residing in the sheets up to the projected pair separation of ∼50 kpc. We observe a complete reversal of this behavior for both the SFR and color of the galaxy pairs having a projected separation larger than 50 kpc. Some earlier studies report that the galaxy pairs align with the filament axis. Such alignment inside filaments indicates anisotropic accretion that may cause these differences. We do not observe these trends in the brighter galaxy samples. The pairs in filaments and sheets from the brighter galaxy samples trace relatively denser regions in these environments. The absence of these trends in the brighter samples may be explained by the dominant effect of the local density over the effects of the large-scale environment.

Astronomy & Astrophysics↗
DOE OSTI2024

Analysis of fusion alphas interaction with RF waves in D-T plasma at JET

This work studies the influence of RF waves in ICRH range of frequency on fusion alphas during the recent JET D-T campaign. Fusion alphas from D-T reactions are born with energies of about 3.5MeV and therefore have significant Doppler shift enabling synergistic interaction between them and RF waves at broad range of frequencies including the ones foreseen for future fusion machines ITER and SPARC. Resonant interaction between RF waves and alphas, also called synergistic effects, will modify the alpha distribution and ultimately will have an impact on alpha orbit losses and heating. Data from JET 3.43T/2.3MA pulses based on the hybrid scenario during the DTE2 campaign were used for the analysis in this study. The impact of synergistic effects on alpha orbit losses and alpha heating is assessed. Conclusions are based on analysis of experimental data for fast alphas losses, i.e. measurements from neutral particle analyser, fast ion losses scintillator detector, Faraday cups, and TRANSP simulations. Experimental data and TRANSP analysis indicate that there are indeed changes in the alphas' distribution function due to interaction with RF waves. Data from the scintillator detector and the Faraday cups were compared for pulses with and without ICRH power and versus cases with enhanced alpha losses due to MHD activities. The trends from these diagnostics consistently show no additional alpha losses due to interaction with RF waves. TRANSP predictions for the impact of the synergistic effects on alpha heating show up to 42% increase in alpha electron heating and up to 25% increase in alpha ion heating. These effects however become negligibly small, less than 1%, when alpha heating is compared to the total auxiliary hearting power in the investigated JET pulses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

ANNIE: Neutron multiplicity in neutrino interactions and new technologies

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) aims at measuring the neutron abundance in the final state of neutrino-nucleus interactions. This measurement will have a direct impact on our understanding of neutrino interactions and will lead to a better reduction of systematic errors and an improvement of signal-background discrimination in future large neutrino detectors, thus impacting long baseline oscillation experiments as well as proton decay searches and supernova detection. With a volume of about 26 tons of pure water doped with gadolinium to enhance neutron tagging efficiency, ANNIE will provide a measurement of the neutron yield of neutrino interactions as a function of the neutrino energy in the well-characterized Booster Neutrino Beam at Fermilab. The modularity of ANNIE will allow it to perform several fundamental tests of new technologies to be used in neutrino detectors, such as a novel kind of photodetectors called Large Area Picosecond Photodetectors and Water-based Liquid Scintillator, a newly-developed detection medium. The technology behind the ANNIE detector will have a noticeable impact on the development of future large water Cherenkov detectors as well as on detection techniques for neutrino physics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Interaction-induced velocity renormalization in magic-angle twisted multilayer graphene

Abstract Twistronics heterostructures provide a novel route to control the electronic single particle velocity and thereby to engineer strong effective interactions. Here we show that the reverse may also hold, i.e. that these interactions strongly renormalize the band structure. We demonstrate this mechanism for alternating-twist magic-angle three- and four-layer graphene at charge neutrality and in the vicinity of a phase transition which can be described by an Ising Gross-Neveu critical point corresponding, e.g. to the onset of valley Hall or Hall order. While the non-interacting model displays massless Dirac excitations with strongly different velocities, we show that interaction corrections make them equal in the infrared. However, the renormalization group flow of the velocities and of the coupling to the critical bosonic mode is strongly non-monotonic and dominated by the vicinity of a repulsive fixed point. We predict experimental consequences of this theory for tunneling and transport experiments and discuss the expected behavior at other quantum critical points, including those corresponding to intervalley coherent ordering.

Classen, Laura↗
DOE OSTI2024

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗
DOE OSTI2026

Dressed-State Hamiltonian Engineering in a Strongly Interacting Solid-State Spin Ensemble

In quantum science applications, ranging from many-body physics to quantum metrology, dipolar interactions in spin ensembles are often controlled via Floquet engineering. However, this technique typically reduces the interaction strength between spins and effectively weakens the coupling to a target sensing field, limiting the metrological sensitivity. In this Letter, we develop and demonstrate an alternative method that directly tunes the native dipolar interaction in an ensemble of nitrogen-vacancy (NV) centers in diamond, thereby overcoming these limitations inherent to Floquet engineering. Our approach utilizes dressed-state qubit encoding under a bias magnetic field applied perpendicular to the crystal lattice orientation. This method leads to a 3.2× enhancement of the dimensionless coherence parameter JT 2 compared to state-of-the-art Floquet engineering and a 2.6× (8.3 dB) enhanced sensitivity in ac magnetometry. Furthermore, our results provide a powerful Hamiltonian engineering tool for future studies with NV ensembles and other interacting higher-spin (S > $\frac{1}{2}$) systems.

Quantum control↗
DOE OSTI2025

Carbon-carbon interactions in warm dense titanium carbide

Encouraged by experimental reports of diamond precipitation in carbon-containing materials under warm dense matter conditions and in shock compression experiments, we examine the behavior of carbon in TiC using density functional theory-molecular dynamics simulations. Two polymorphs of TiC are considered, the ambient-pressure B1 ($Fm$$\overline{3}$$m$) structure in which C-C interactions are prevented by geometric constraints, and a high-pressure Cmcm structure in which C atoms condense into zigzag chains. Chemistry-inspired bonding analyses confirm the covalently bound nature of these chains and further illuminate important interatomic interactions in both structures. Upon melting of B1 TiC, new short-range C-C interactions develop in the liquid, while the pre-existing C-C interactions in Cmcm TiC persist in the liquid. Here, the resulting carbon networks in the melt provide a promising environment for eventual diamond nucleation.

Ab initio molecular dynamics↗
DOE OSTI2023

Modeling noise in global Mølmer-Sørensen interactions applied to quantum approximate optimization

Many-qubit Mølmer-Sørensen (MS) interactions applied to trapped ions offer unique capabilities for quantum information processing, with applications including quantum simulation and the quantum approximate optimization algorithm (QAOA). Here, we develop a physical model to describe many-qubit MS interactions under four sources of experimental noise: vibrational mode frequency fluctuations, laser power fluctuations, thermal initial vibrational states, and state preparation and measurement errors. The model parametrizes these errors from simple experimental measurements, without free parameters. Herein, we validate the model in comparison with experiments that implement sequences of MS interactions on two 171 Yb + ions. The model shows reasonable agreement after several MS interactions as quantified by the reduced chi-squared statistic $χ^{2}_{red}$≈2. As an application we examine MaxCut QAOA experiments on three and six ions. The experimental performance is quantified by approximation ratios that are 91% and 83% of the optimal theoretical values. Our model predicts $0.93^{+0.03}_{-0.02}$ and $0.95^{+0.04}_{-0.03}$, respectively, with disagreement in the latter value attributable to secondary noise sources beyond those considered in our analysis. With realistic experimental improvements to reduce measurement error and radial trap frequency variations, the model achieves approximation ratios that are 99% of the optimal. Incorporating these improvements into future experiments is expected to reveal new aspects of noise for future modeling and experimental improvements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Magnetic structure and exchange interactions in the layered semiconductor CrPS 4

Compounds with two-dimensional (2D) layers of magnetic ions weakly connected by van der Waals bonding offer routes to enhance quantum behavior, stimulating both fundamental and applied interest. CrPS 4 is one such magnetic van der Waals material, however, it has undergone only limited investigation. Here we present a comprehensive series of neutron scattering measurements to determine the magnetic structure and exchange interactions. The observed magnetic excitations allow a high degree of constraint on the model parameters not normally associated with measurements on a powder sample. The results demonstrate the 2D nature of the magnetic interactions, while also revealing the importance of interactions along 1D chains within the layers. The subtle role of competing interactions is observed, which manifest in a nontrivial magnetic transition and a tunable magnetic structure in a small applied magnetic field through a spin-flop transition. Our results on the bulk compound provide insights that can be applied to an understanding of the behavior of reduced layer CrPS 4 .

36 MATERIALS SCIENCE↗
DOE OSTI2020

Image charge interaction correction in charged-defect calculations

Charged-defect calculation using a periodic supercell is a significant class of problems in solid state physics. However, the finite supercell size induces an undesirable long-range image charge Coulomb interaction. Although a variety of methods have been proposed to eliminate such image Coulomb interaction, most of the previous schemes are based on a rough approximation of the defect charge screening. In this work, we present a rigorous derivation of the image charge interaction with a defect screening model where the use of a bulk macroscopic dielectric constant can be avoided. Here, we have verified this approach in comparison with a widely used approach for 12 different defects. Our correction scheme offers a much faster convergence concerning the supercell size for cases with considerable image charge interactions. In those cases, we also found that the nonlinear dielectric screening might play an important role. Our proposed defect screening model will also shed new light on understanding the defect screening properties and can be applied to other defect systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗