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At least 1,639 records · Page 91
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Ripple-induced neoclassical toroidal viscous torque in Augmented-First Plasma operation phase in ITER

Abstract A systematic calculation is performed on the ripple-induced neoclassical toroidal viscous (NTV) torque for new ITER scenarios designed for the Augmented-First Plasma (A-FP) operation phase with the full tungsten wall, where the plasma-wall gap is varied in view of mitigating the impact of tungsten wall-plasma interactions. The torque calculation includes drift kinetic response of the plasma thermal and energetic particles to the n = 18 ( n is the toroidal harmonic number) ripple field. For the plasma scenario with ~45 cm plasma-wall gap at the outboard mid-plane and considering the corrected ripple level of 0.17% by the ferritic steel inserts, the computed net NTV torque acting on the plasma column is in the sub-Nm level. However, with decreasing the plasma-wall gap, the computed net NTV torque can reach a level comparable to that produced by the neutral-beam momentum injection in ITER. Ripple correction by ferritic inserts reduces the net torque by a factor of 3.3 for all the three A-FP scenarios considered. The n ω d = l ω b (with ω d and ω b being the toroidal precession and bounce frequencies of trapped particles, respectively, and l an integer number) type of resonance-enhancement of the NTV torque, due to thermal particles, is found to be weak in ITER despite high- n of 18. The same also holds for the ITER 10 MA steady state scenario from the D-T operation phase, where the aforementioned resonance associated with fusion-born alphas is also included. The ripple-induced NTV torque is well below that produced by the resonant magnetic perturbation applied for controlling the type-I edge-localized mode in ITER.

ITER↗
DOE OSTI2019

More exact results in the Wilson loop defect CFT: bulk-defect OPE, nonplanar corrections and quantum spectral curve

We perform here exact computations of correlation functions of 1/2-BPS local operators and protected operator insertions on the 1/8-BPS Wilson loop in $\mathcal{N}=4$ SYM. This generalizes the results of our previous paper arXiv:1802.05201, which employs supersymmetric localization, OPE and the Gram-Schmidt process. In particular, we conduct a detailed analysis for the 1/2-BPS circular (or straight) Wilson loop in the planar limit, which defines an interesting nontrivial defect CFT. We compute its bulk-defect structure constants at finite 't Hooft coupling, and present simple integral expressions in terms of the $Q$-functions that appear in the Quantum Spectral Curve---a formalism originally introduced for the computation of the operator spectrum. The results at strong coupling are found to be in precise agreement with the holographic calculation based on perturbation theory around the AdS$_2$ string worldsheet, where they correspond to correlation functions of open string fluctuations and closed string vertex operators inserted on the worldsheet. Along the way, we clarify several aspects of the Gram-Schmidt analysis which were not addressed in the previous paper. Specifically, we clarify the role played by the multi-trace operators at the non-planar level, and confirm its importance by computing the non-planar correction to the defect two-point function. We also provide a formula for the first non-planar correction to the defect correlators in terms of the Quantum Spectral Curve, which suggests the potential applicability of the formalism to the non-planar correlation functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Femtosecond laser fabrication of nanograting-based distributed fiber sensors for extreme environmental applications

Abstract The femtosecond laser has emerged as a powerful tool for micro- and nanoscale device fabrication. Through nonlinear ionization processes, nanometer-sized material modifications can be inscribed in transparent materials for device fabrication. This paper describes femtosecond precision inscription of nanograting in silica fiber cores to form both distributed and point fiber sensors for sensing applications in extreme environmental conditions. Through the use of scanning electron microscope imaging and laser processing optimization, high-temperature stable, Type II femtosecond laser modifications were continuously inscribed, point by point, with only an insertion loss at 1 dB m −1 or 0.001 dB per point sensor device. High-temperature performance of fiber sensors was tested at 1000 °C, which showed a temperature fluctuation of ±5.5 °C over 5 days. The low laser-induced insertion loss in optical fibers enabled the fabrication of a 1.4 m, radiation-resilient distributed fiber sensor. The in-pile testing of the distributed fiber sensor further showed that fiber sensors can execute stable and distributed temperature measurements in extreme radiation environments. Overall, this paper demonstrates that femtosecond-laser-fabricated fiber sensors are suitable measurement devices for applications in extreme environments.

Wang, Mohan (ORCID:0000000166784993)↗
DOE OSTI2024

Atomic-scale oxygen-vacancy engineering in Sub-2 nm thin Al 2 O 3 /MgO memristors

Ultrathin (sub-2 nm) Al 2 O 3 /MgO memristors were recently developed using an in vacuo atomic layer deposition (ALD) process that minimizes unintended defects and prevents undesirable leakage current. These memristors provide a unique platform that allows oxygen vacancies (V O ) to be inserted into the memristor with atomic precision and study how this affects the formation and rupture of conductive filaments (CFs) during memristive switching. Herein, we present a systematic study on three sets of ultrathin Al 2 O 3 /MgO memristors with V O -doping via modular MgO atomic layer insertion into an otherwise pristine insulating Al 2 O 3 atomic layer stack (ALS) using an in vacuo ALD. At a fixed memristor thickness of 17 Al 2 O 3 /MgO atomic layers (~1.9 nm), the properties of the memristors were found to be affected by the number and stacking pattern of the MgO atomic layers in the Al 2 O 3 /MgO ALS. Importantly, the trend of reduced low-state resistance and the increasing appearance of multi-step switches with an increasing number of MgO atomic layers suggests a direct correlation between the dimension and dynamic evolution of the conducting filaments and the V O concentration and distribution. Understanding such a correlation is critical to an atomic-scale control of the switching behavior of ultrathin memristors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗
DOE OSTI2017

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stress-regulated Arabidopsis GAT2 is a low affinity γ-aminobutyric acid transporter

Abstract The four-carbon non-proteinogenic amino acid γ-aminobutyric acid (GABA) accumulates to high levels in plants in response to various abiotic and biotic stress stimuli, and plays a role in C:N balance, signaling, and as a transport regulator. Expression in Xenopus oocytes and voltage-clamping allowed the characterization of Arabidopsis GAT2 (At5g41800) as a low affinity GABA transporter with a K0.5GABA ~8 mM. l-Alanine and butylamine represented additional substrates. GABA-induced currents were strongly dependent on the membrane potential, reaching the highest affinity and highest transport rates at strongly negative membrane potentials. Mutation of Ser17, previously reported to be phosphorylated in planta, did not result in altered affinity. In a short-term stress experiment, AtGAT2 mRNA levels were up-regulated at low water potential and under osmotic stress (polyethylene glycol and mannitol). Furthermore, AtGAT2 promoter activity was detected in vascular tissues, maturating pollen, and the phloem unloading region of young seeds. Even though this suggested a role for AtGAT2 in long-distance transport and loading of sink organs, under the conditions tested neither AtGAT2-overexpressing plants, atgat2 or atgat1 T-DNA insertion lines, nor atgat1 atgat2 doubleknockout mutants differed from wild-type plants in growth on GABA, amino acid levels, or resistance to salt and osmotic stress.

Plant Sciences↗
DOE OSTI2024

Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer

Abstract 5-Fluorouracil (5-FU) is the first-line chemotherapeutic agent in colorectal cancer, and resistance to 5-FU easily emerges. One of the mechanisms of drug action and resistance of 5-FU is through DNA incorporation. Our quantitative reverse-transcription PCR data showed that one of the translesion synthesis (TLS) DNA polymerases, DNA polymerase η (polη), was upregulated within 72 h upon 5-FU administration at 1 and 10 μM, indicating that polη is one of the first responding polymerases, and the only TLS polymerase, upon the 5-FU treatment to incorporate 5-FU into DNA. Our kinetic studies revealed that 5-fluoro-2′-deoxyuridine triphosphate (5FdUTP) was incorporated across dA 41 and 28 times more efficiently than across dG and across inosine, respectively, by polη indicating that the mutagenicity of 5-FU incorporation is higher in the presence of inosine and that DNA lesions could lead to more mutagenic incorporation of 5-FU. Our polη crystal structures complexed with DNA and 5FdUTP revealed that dA:5FdUTP base pair is like dA:dTTP in the active site of polη, while 5FdUTP adopted 4-enol tautomer in the base pairs with dG and HX increasing the insertion efficiency compared to dG:dTTP for the incorrect insertions. These studies confirm that polη engages in the DNA incorporation and bypass of 5-FU.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine

N7-Methyl-2 -deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2 -fluorine-mediated transitionstate destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2 -fluorom7dG (Fm7dG), by human DNA polymerase (pol) and solved three X-ray structures of pol in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows pol catalysis ~300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson–Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the pol-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by pol. In addition, the pol-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7- methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that pol catalysis across m7dG is slow, yet highly accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus

Abstract Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗
DOE OSTI2024

Error mitigation, optimization, and extrapolation on a trapped-ion testbed

Current noisy intermediate-scale quantum (NISQ) trapped-ion devices are subject to errors which can significantly impact the accuracy of calculations if left unchecked. A form of error mitigation called zero noise extrapolation (ZNE) can decrease an algorithm’s sensitivity to these errors without increasing the number of required qubits. Here we explore different methods for integrating this error mitigation technique into the Variational Quantum Eigensolver (VQE) algorithm for calculating the ground state of the HeH + molecule at 0.8 Å in the presence of experimental noise. Using the Quantum Scientific Computing Open User Testbed (QSCOUT) trapped-ion device, we test three methods of scaling noise for extrapolation: time stretching the two-qubit gates, scaling the sideband detuning parameter, and inserting two-qubit gate identity operations into the ansatz circuit. We find that time stretching and sideband detuning scaling fail to scale the noise on our particular hardware in a way that can be extrapolated to zero noise. Scaling our noise with global gate identity insertions and extrapolating after variational optimization, we achieve error suppression of 96.8%, resulting in an energy estimate within –0.004 ± 0.04 hartree of the ground state energy. This is an improvement, but still outside the chemical accuracy threshold of 0.0016 hartree. Furthermore, our results show that the efficacy of this error mitigation technique depends on choosing the correct implementation for a given device architecture.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Enhanced orbital anisotropy through the proximity to a SrTiO 3 layer in the perovskite iridate superlattices

We have used angle-dependent soft x-ray absorption spectroscopy (XAS) at the O K edge and first-principles calculations to investigate the electronic structures of iridate-based superlattices ( SrIr O 3 ) m / ( SrTi O 3 ) ( m = 1 , 2, 3, and ∞). We focus on the pre-edge Ir 5 d t 2 g – O 2 p orbital hybridization feature in the XAS spectra. By varying the measurement geometry relative to the incident photon polarization, we are able to extract the dichroic contrast and observe the systematic increase in the anisotropy of Ir 5 d orbitals as m decreases. First-principles calculations elucidate the orbital anisotropy coming mainly from the enhanced out-of-plane compression of Ir O 6 octahedra in the SrIr O 3 layers that are adjacent to the inserted SrTi O 3 layers. As m decreases, the increased volume fraction of these interfacial SrIr O 3 layers and their contact with the SrTi O 3 layers within the ( SrIr O 3 ) m / ( SrTi O 3 ) supercell lead to enhanced orbital anisotropy. Furthermore, the tilt and rotation of Ir O 6 octahedra are shown to be essential to understand the subtle orbital anisotropy in these superlattices, and constraining these degrees of freedom will give an incorrect trend. Overall, our results demonstrate that the structural constraint from the inserted SrTi O 3 layers, in addition to other electronic means such as polar interface and charge transfer, can serve as a knob to control the orbital degree of freedom in these iridate-based superlattices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Magnetic damping in ferromagnetic/heavy-metal systems: The role of interfaces and the relation to proximity-induced magnetism

Damping and spin transport in spintronic multilayered systems continues to be a topic of active research. The enhancement of damping in ferromagnet (FM)/spacer layer (SL)/heavy-metal (HM) thin-film systems was studied for Co 25 Fe 75 /SL/Pt with a nonmagnetic (NM) SL of either Au or Cu with variable thickness, in order to understand the correlation with proximity-induced magnetism (PIM) in the HM. Structural, PIM and magnetic damping measurements were undertaken on the same samples. Specifically, secondary ion mass spectroscopy, element specific x-ray magnetic reflectivity and x-ray magnetic circular dichroism at the Pt and Au L 3 edges, and ferromagnetic resonance methods were used. With increasing thickness of a Cu or Au SL directly between the FM and the Pt layer, the Pt PIM and the damping both fall rapidly, with a relationship between damping and PIM that depends on the SL material. The PIM observed in the Au layer showed a complex dependence on the layer thickness, suggesting some hybridization with the Pt. The role of the number and location of interfaces on the damping was demonstrated with the addition of a SL within the Pt layer, which showed that the specific details of the NM/HM interface also affects the damping. The insertion of a Cu SL within the Pt showed a measurable increase in the overall enhancement of the damping while the insertion of a Au SL into Pt had almost no effect on the damping. Finally, together these results demonstrate the role of both PIM and of additional interfaces in the enhancement of damping in FM/HM systems, which is not fully accounted for by existing theory

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Anomalous Hall hysteresis in Tm 3 Fe 5 O 12 /Pt with strain-induced perpendicular magnetic anisotropy

Here we demonstrate robust interface strain-induced perpendicular magnetic anisotropy in atomically flat ferrimagnetic insulator Tm 3 Fe 5 O 12 (TIG) films grown with pulsed laser deposition on a substituted Gd 3 Ga 5 O 12 substrate which maximizes the tensile strain at the interface. In bilayers consisting of Pt and TIG, we observe large squared Hall hysteresis loops over a wide range of thicknesses of Pt at room temperature. When a thin Cu layer is inserted between Pt and TIG, the Hall hysteresis magnitude decays but stays finite as the thickness of Cu increases up to 5 nm. However, if the Cu layer is placed atop Pt instead, the Hall hysteresis magnitude is consistently larger than when the Cu layer with the same thickness is inserted in between for all Cu thicknesses. These results suggest that both the proximity-induced ferromagnetism and spin current contribute to the anomalous Hall effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Interfacial control of Dzyaloshinskii-Moriya interaction in heavy metal/ferromagnetic metal thin film heterostructures

The interfacial Dzyaloshinskii-Moriya interaction (DMI) in ultrathin magnetic thin film heterostructures provides a new approach for controlling spin textures on mesoscopic length scales. Here we investigate the dependence of the interfacial DMI constant D on a Pt wedge insertion layer in Ta/CoFeB/Pt(wedge)/MgO thin films by observing the asymmetric spin-wave dispersion using Brillouin light scattering. Continuous tuning of D by more than a factor of 3 is realized by inserting less than one monolayer of Pt. The observations in this work provide new insights for designing magnetic thin film heterostructures with tailored D for controlling skyrmions and magnetic domain-wall chirality and dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Exact evaluation of large-charge correlation functions in nonrelativistic conformal field theory

The large-charge master field which generates all n -point correlation functions with an insertion of large charge Q in nonrelativistic conformal field theory is obtained. This field is used to compute Schrödinger-invariant n -point correlation functions of large-charge operators via a direct evaluation of the path integral. Conformal dimensions are found to agree with calculations based on the state-operator correspondence. The master field solution exhibits an emergent harmonic trap whose frequency is a function of the Euclidean time. The large-charge effective action with operator insertions describes a droplet of superfluid matter whose spatial size scales with the time separation of sources. The solution is used to compute Schrödinger symmetry breaking corrections in the large-charge effective field theory (EFT) due to a finite scattering length in the fundamental theory of fermions near unitarity. The scaling of these effects in the large-charge power counting scheme is established, and the size of the effects is quantified using input from quantum Monte Carlo simulations of the near-unitary gas, as well as from the large- N expansion at large charge. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2018

Dispersion-Based Fresh-Slice Scheme for Free-Electron Lasers

The fresh-slice technique improved the performance of several self-amplified spontaneous emission free-electron laser schemes by granting selective control on the temporal lasing slice without spoiling the other electron bunch slices. So far, the implementation has required a special insertion device to create the beam yaw, called a dechirper. Finally, we demonstrate a novel scheme to enable fresh-slice operation based on electron energy chirp and orbit dispersion that can be implemented at any free-electron laser facility without additional hardware.

47 OTHER INSTRUMENTATION↗