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At least 235 records · Page 13

A general framework for substructuring-based domain decomposition methods for models having nonlocal interactions [including apppendix B]

A rigorous mathematical framework is provided for a substructuring-based domain-decomposition approach for nonlocal problems that feature interactions between points separated by a finite distance. Here, by substructuring it is meant that a traditional geometric configuration for local partial differential equation problems is used in which a computational domain is subdivided into non-overlapping subdomains. In the nonlocal setting, this approach is substructuring-based in the sense that those subdomains interact with neighboring domains over interface regions having finite volume, in contrast to the local PDE setting in which interfaces are lower dimensional manifolds separating abutting subdomains Key results include the equivalence between the global, single-domain nonlocal problem and its multi-domain reformulation, both at the continuous and discrete levels. These results provide the rigorous foundation necessary for the development of efficient solution strategies for nonlocal domain-decomposition methods.

97 MATHEMATICS AND COMPUTING↗

Laboratory Instrument Software Controlled Spread Spectrum Time Domain Reflectometry for Electrical Cable Testing

This research discusses development of a software-controlled laboratory instrument based spread spectrum time domain reflectometry system (SSTDR). This constitutes one task within PNNL’s Light Water Sustainability Program (LWRS) whose mission includes advancing nondestructive examination (NDE) techniques for off-line and on-line in-situ cable condition monitoring. In 2022, PNNL evaluated SSTDR for detection and characterization of a number of cable anomalies (Glass et al. 2022). The review included comparison of SSTDR to Frequency Domain Reflectometry (FDR) techniques which have enjoyed encouraging feedback and are starting to be used in nuclear power plants for periodic cable condition monitoring of cable systems as part of the plant’s overall cable aging management program. The FDR test introduces a broad-band chirp onto the cable at the cable end then listens for any reflection from a change of impedance along the cable caused by a damaged conductor or insulation, splices, contact with moisture, or other cable anomalies. The signal is captured in the frequency domain then transformed back to the time domain using an inverse Fourier transform (IFT). Based on the velocity of propagation, the impedance response signal is plotted against distance along the cable. Peak locations along the X-axis indicate the distance along the cable where a portion of the signal has been reflected back to the instrument as a result of a cable anomaly. The FDR test is considered the gold standard of reflectometry however it does require the cable to be de-energized to perform the test. The LIVEWIRE commercial SSTDR produces a similar plot to the FDR however all processing is in the time domain. A pseudo-random noise code (PN code) is input onto the cable conductor and the instrument listens for any reflected response from cable anomalies. The SSTDR processes the signal as an autocorrelation comparing the input PN code to any reflected signal detected. The autocorrelation analysis for thermal aging, water and water ingress detection, ground fault and phase-to-phase fault detection at various locations along the cable and with the cable attached and detached from a motor load, and on both energized and un-energized conditions were performed. These results were contrasted to Frequency Domain Reflectometry (FDR) measurements of the un-energized cable. Results were encouraging but indicated more work was warranted – particularly with the SSTDR, it seemed that the insulation damage would likely be better evaluated with multiple bandwidth cable tests particularly including larger bandwidths than were possible with the current commercial instrument. The commercial instrument’s bandwidth was set at 6, 12, 24, and 48MHz but note that SSTDR and FDR definitions of bandwidth trend similarly but are not the same. The FDR response could be more broadly adjusted, and the bandwidth of 100 to 500 MHz produced the best responses. FDR responses to anomalies were clearer than SSTDR responses and indications were that a broader bandwidth SSTDR may lead to improved SSTDR detection capability. This project used a laboratory instrument based SSTDR (primarily using an Arbitrary Waveform Generator (AWG) and a digital oscilloscope plus Python in-house software) that allowed software adjustment of the SSTDR bandwidth, window functions applied to the exciting Pseudo-random Noise (PN) code plus and other aspects of the SSTDR signal processing. Hereafter, this will be referred to as the PNNL SSTDR. Evaluating specific performance of the PNNL SSTDR is left to a separate report. This report documents hardware and software development to produce the SSTDR cable test system.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Spontaneous Asymmetry of Chiral Magnetic Domains Within a Magnetic Field

Abstract Chiral magnetic domains are topological spin textures in which the Dzyaloshinskii–Moriya interaction assigns a given chirality to the domain walls. Notably, despite rapid progress in chiral magnetic research, one fundamental issue that remains unclear is how the chirality of chiral magnetic domains change as a magnetic field deforms the spin texture. Using spin‐polarized low energy electron microscopy, the evolution of Fe/Ni chiral magnetic stripe domains are investigated in single‐crystalline Fe/Ni/Cu/Co/Cu(001) multilayers in which the interlayer magnetic coupling between the Co and Fe/Ni films serves as an in‐plane magnetic field. Contrary to theoretical works, it is found that the chirality of the Néel walls results in a parallel alignment of the magnetic stripes with the in‐plane magnetic field direction. The transformation of chiral Néel walls into achiral Bloch walls can be precisely controlled by tuning the Cu spacer layer thickness. In addition, the domain wall exhibits a spontaneous asymmetry within the in‐plane magnetic field, leading to an unbalanced chirality between the left‐handed and right‐handed Bloch walls. These new results foster a better understanding of the chiral domain properties within a magnetic field.

Li, Qian↗

Ferroelectric Domain Wall Engineering Enables Thermal Modulation in PMN–PT Single Crystals

Acting like thermal resistances, ferroelectric domain walls can be manipulated to realize dynamic modulation of thermal conductivity ( k ), which is essential for developing novel phononic circuits. Despite the interest, little attention has been paid to achieving room-temperature thermal modulation in bulk materials due to challenges in obtaining a high thermal conductivity switching ratio ( k high / k low ), particularly in commercially viable materials. Here, room-temperature thermal modulation in 2.5 mm-thick Pb(Mg 1/3 Nb 2/3 )O 3 – x PbTiO 3 (PMN– x PT) single crystals is demonstrated. With the use of advanced poling conditions, assisted by the systematic study on composition and orientation dependence of PMN– x PT, a range of thermal conductivity switching ratios with a maximum of ≈1.27 is observed. Further, simultaneous measurements of piezoelectric coefficient (d 33 ) to characterize the poling state, domain wall density using polarized light microscopy (PLM), and birefringence change using quantitative PLM reveal that compared to the unpoled state, the domain wall density at intermediate poling states (0< d 33 33,max ) is lower due to the enlargement in domain size. At optimized poling conditions (d 33,max ), the domain sizes show increased inhomogeneity that leads to enhancement in the domain wall density. This work highlights the potential of commercially available PMN– x PT single crystals among other relaxor-ferroelectrics for achieving temperature control in solid-state devices.

36 MATERIALS SCIENCE↗

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗

Interaction of cosmological domain walls with large classical objects, like planets and satellites, and the flyby anomaly

Cosmological domain walls can be formed as a result of symmetry breaking at any epoch during the evolution of our universe. We study their interaction with a classical macroscopic object, like Earth or a satellite in Earth’s orbit. We set up an action that includes the interaction term between the massive classical object and the scalar field that the domain wall is made of. We use numerical calculations to solve the coupled equations of motion which describe the crossing between the domain wall and the classical object. Depending on the strength of the interaction, relative velocity and size, the object can be either stopped by the wall, or it can pass through it inducing deformations in the wall that cost energy. At the same time, the coupling to the scalar filed might change the object’s mass during the crossover. The fact that satellites in Earth’s orbit (or planets in Sun’s orbit) can change their mass and/or lose energy interacting with walls can be used as a new domain wall detection probe. For example, a typical velocity precision of a satellite is about 0.5 mm/s, which directly puts an upper limit on its mass change to ΔM/M ≲ 5 × 10 –17 . Alternatively, a known satellite flyby anomaly can easily be explained as an interaction with a closed domain wall. We also show that the presence of matter modifies the scalar filed potential and can locally create a bubble of the true vacuum, and thus trigger the decay of the false vacuum. For a critical bubble which is able to expand, such an interaction with the domain wall must be strong enough.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

QCD-collapsed domain walls: QCD phase transition and gravitational wave spectroscopy

Abstract For a discrete symmetry that is anomalous under QCD, the domain walls produced in the early universe from its spontaneous breaking can naturally annihilate due to QCD instanton effects. The gravitational waves generated from wall annihilation have their amplitude and frequency determined by both the discrete symmetry breaking scale and the QCD scale. The evidence of stochastic gravitational waves at nanohertz observed by pulsar timing array experiments suggests that the discrete-symmetry-breaking scale is around 100 TeV, assuming the domain-wall explanation. The annihilation temperature is about 100 MeV, which could naturally be below the QCD phase transition temperature. We point out that the QCD phase transition within some domains with an effective large QCDθangle could be a first-order one. To derive the phase diagram inθand temperature, we adopt a phenomenological linear sigma model with three quark flavors. The domain-wall explanation for the NANOGrav, EPTA, PPTA and CPTA results hints at a first-order QCD phase transition, which predicts additional gravitational waves at higher frequencies. If the initial formation of domain walls is also a first-order process, this class of domain-wall models predicts an interesting gravitational wave spectroscopy with frequencies spanning more than ten orders of magnitude, from nanohertz to 100 Hz.

Physics↗

Field-Dependent Magnetic Domain Behavior in van der Waals Fe 3 GeTe 2

Two-dimensional magnetic van der Waals (vdW) materials can show a variety of topological nontrivial spin textures, such as Bloch- or Néel-type stripe, skyrmion, or bubble domains under certain external stimuli. It is critical to understand the magnetic domain behavior in vdW materials in order to control their size and density in response to external stimuli, such as electric and magnetic fields. In this study, we examine the magnetic field dependence of topologically non-trivial magnetization spin textures in vdW Fe 3 GeTe 2 . Néel-type stripe domains and skyrmions are formed depending on the magnetic field-cooling protocol used during in situ Lorentz transmission electron microscopy (LTEM) experiments. Use of quantitative reconstruction of magnetic induction maps and micromagnetic simulations allow for the understanding of the LTEM results of Néel-type stripe domains as well as skyrmions. In addition, the deformation of skyrmion contrast is observed as a result of the introduction of an in-plane magnetic field. We demonstrate the stability of the stripe domains and skyrmions in response to an externally applied magnetic field due to an energy barrier for domain wall annihilation. Our results establish an understanding of the energy landscape that governs the behavior of the topologically non-trivial spin textures in vdW materials which can be harnessed for spintronic applications.

36 MATERIALS SCIENCE↗

A quasi-meshfree method for constructing boundary-aware reproducing bases on geometrically complex domains using manifold geodesics

In many applications, physical domains are geometrically complex making it challenging to perform coarse-scale approximation. A defeaturing process is often used to simplify the domain in preparation for approximation and analysis at the coarse scale. In this paper, a methodology is presented for constructing a coarse-scale reproducing basis on geometrically complex domains given an initial fine-scale mesh of the fully featured domain. The initial fine-scale mesh can be of poor quality and extremely refined. The construction of the basis functions begins with a coarse-scale covering of the domain and generation of weighting functions with local support. Manifold geodesics are used to define distances within the local support for general applicability to non-convex domains. Conventional moving least squares is used to construct the coarse-scale reproducing basis. Applications in quasi-interpolation and linear elasticity are presented.

97 MATHEMATICS AND COMPUTING↗

Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase

Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg 2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sim-to-real supervised domain adaptation for radioisotope identification

Machine learning has the potential to improve the speed and reliability of radioisotope identification using gamma spectroscopy. However, meticulously labeling an experimental dataset for training is often prohibitively expensive, while training models purely on synthetic data is risky due to the domain gap between simulated and experimental measurements. In this research, we demonstrate that supervised domain adaptation can substantially improve the performance of radioisotope identification models by transferring knowledge between synthetic and experimental data domains. We consider two domain adaptation scenarios: (1) a simulation-to-simulation adaptation, where we perform multi-label proportion estimation using simulated high-purity germanium detectors, and (2) a simulation-to-experimental adaptation, where we perform multi-class, single-label classification using measured spectra from handheld lanthanum bromide (LaBr) and sodium iodide (NaI) detectors. We begin by pretraining a spectral classifier on synthetic data using a custom transformer-based neural network. After subsequent fine-tuning on just 64 labeled experimental spectra, we achieve a test accuracy of 96% in the sim-to-real scenario with a LaBr detector, far surpassing a synthetic-only baseline model (75%) and a model trained from scratch (80%) on the same 64 spectra. Furthermore, we demonstrate that domain-adapted models learn more human-interpretable features than experiment-only baseline models. Overall, our results highlight the potential for supervised domain adaptation techniques to bridge the sim-to-real gap in radioisotope identification, enabling the development of accurate and explainable classifiers even in real-world scenarios where access to experimental data is limited.

Lalor, Peter W.↗

Association of somatic mutations in BRCA2 BRC domain with chemotherapy sensitivity and survival in high grade serous ovarian cancer

Highlights: • BRCA2 BRC domain-associated mutation confers higher platinum sensitivity of HGSOC. • Somatic BRCA2 BRC domain mutation impairs BRCA2 HR in HGSOC. • BRCA2 BRC domain mutation at sites is crucial for HR repair of DNA DSB induced by platinums. • Somatic BRCA2 BRC domain missense mutations improve outcomes in patients with HGSOC. Mutations at sites crucial for the interaction between RAD51 and BRC domains impair the ability of BRCA2 homologous recombination. We aimed to clarify whether BRCA2 BRC domain-associated mutation correlates with sensibility of platinum-based chemotherapy and survival in high-grade serous ovarian cancer (HGSOC).

60 APPLIED LIFE SCIENCES↗

Bounce-averaged theory in arbitrary multi-well plasmas: solution domains and the graph structure of their connections

Bounce-averaged theories provide a framework for simulating relatively slow processes, such as collisional transport and quasilinear diffusion, by averaging these processes over the fast periodic motions of a particle on a closed orbit. This procedure dramatically increases the characteristic time scale and reduces the dimensionality of the modelled system. The natural coordinates for such calculations are the constants of motion (COM) of the fast particle motion, which by definition do not change during an orbit. However, for sufficiently complicated fields – particularly in the presence of local maxima of the electric potential and magnetic field – the COM are not sufficient to specify the particle trajectory. In such cases, multiple domains in COM space must be used to solve the problem, with boundary conditions enforced between the domains to ensure continuity and particle conservation. Previously, these domains have been imposed by hand, or by recognising local maxima in the fields, limiting the flexibility of bounce-averaged simulations. Here, we present a general set of conditions for identifying consistent domains and the boundary condition connections between the domains, allowing the application of bounce-averaged theories in arbitrarily complicated and dynamically evolving electromagnetic field geometries. We also show how the connections between the domains can be represented by a directed graph, which can help to succinctly represent the trajectory bifurcation structure.

fusion plasma↗

Macroscopic Monochalcogenide van der Waals Ferroics: Growth, Domain Structures, and Curie Temperature

Two-dimensional and layered van der Waals materials promise to overcome the limitations of conventional ferroelectrics in terms of miniaturization and material integration, but synthesis has produced only small (up to few micrometer-sized) ferroic crystals. Here, we report the realization of in-plane ferroelectric few-layer crystals of the monochalcogenides tin(II) sulfide and selenide (SnS, SnSe) whose linear dimensions exceed the current state of the art by up to 1 order of magnitude. Such large crystals allow the investigation of ferroic domain patterns that are unaffected by edges and finite-size effects. Analysis of the abundant stripe domains by electron microscopy and nanobeam electron diffraction shows two distinct domain types: twin domains separated by positively charged walls with alternating head-to-head and tail-to-tail polarization as well as not previously observed purely rotational domains connected by neutral domain walls with head-to-tail dipoles. Access to large crystals allowed the determination of the Curie temperature of few-layer SnSe van der Waals ferroelectrics, and it enables the investigation of this class of ferroelectrics by widely available methods such as polarized optical microscopy. Furthermore, the combination with layer transfer protocols promises uniform materials for exploring fundamentals and for implementing devices for information processing and energy conversion.

36 MATERIALS SCIENCE↗

Influences of North Pacific Ocean Domain Extent on the Western U.S. Winter Hydroclimatology in Variable-Resolution CESM

Variable-resolution global climate models (VRGCMs) are a dynamical downscaling method that can reach spatiotemporal scales needed for regional climate assessments. Over the years, several users of VRGCMs have assumed where the location and extent of the refinement domain should be based on knowledge of the prevailing storm tracks and resolution dependence of important regional climate processes (e.g., atmospheric rivers [ARs] and orographic uplift), but the effect of high-resolution domain size and extent on the simulation of downstream hydroclimatic phenomena has not been systematically evaluated. Here, we use variable resolution in the Community Earth System Model (VR-CESM) to perform such a test. To do this, three VR-CESM grids were generated that span the entire, two thirds, and one third of the North Pacific and evaluated for a 30-year climatology using Atmospheric Model Intercomparison Project protocols. Simulations are compared with reanalysis products offshore (fifth-generation of the European Centre for Medium-Range Weather Forecasts atmospheric reanalysis [ERA5]) and onshore (Livneh, 2015, https://doi.org/10.1038/sdata.2015.42, and Parameter-elevation Regressions on Independent Slopes Model [PRISM]) of the western United States. The westward expansion of refinement domain influenced integrated vapor transport (IVT), which was generally high biased but minimally impacted AR characteristics. Due to slight differences in landfalling AR counts in the western United States, California winter precipitation generally improved with westward expansion of the refinement domain. Western U.S. mountain snowpack and surface temperatures were insensitive to refinement domain size and were more influenced by changes in topographic resolution and/or land surface model version. Here, given minimal dependence of simulated western U.S. hydroclimate on refinement domain size over the North Pacific, we advise future VR-CESM studies to focus grid resolution on better resolving land surface heterogeneity.

54 ENVIRONMENTAL SCIENCES↗

The emergence of three-dimensional chiral domain walls in polar vortices

Abstract Chirality or handedness of a material can be used as an order parameter to uncover the emergent electronic properties for quantum information science. Conventionally, chirality is found in naturally occurring biomolecules and magnetic materials. Chirality can be engineered in a topological polar vortex ferroelectric/dielectric system via atomic-scale symmetry-breaking operations. We use four-dimensional scanning transmission electron microscopy (4D-STEM) to map out the topology-driven three-dimensional domain walls, where the handedness of two neighbor topological domains change or remain the same. The nature of the domain walls is governed by the interplay of the local perpendicular (lateral) and parallel (axial) polarization with respect to the tubular vortex structures. Unique symmetry-breaking operations and the finite nature of domain walls result in a triple point formation at the junction of chiral and achiral domain walls. The unconventional nature of the domain walls with triple point pairs may result in unique electrostatic and magnetic properties potentially useful for quantum sensing applications.

36 MATERIALS SCIENCE↗

Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries

Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

59 BASIC BIOLOGICAL SCIENCES↗

Reversible long-range domain wall motion in an improper ferroelectric

Reversible ferroelectric domain wall movements beyond the 10 nm range associated with Rayleigh behavior are usually restricted to specific defect-engineered systems. Here, we demonstrate that such long-range movements naturally occur in the improper ferroelectric ErMnO 3 during electric-field-cycling. We study the electric-field-driven motion of domain walls, showing that they readily return to their initial position after having traveled distances exceeding 250 nm. By applying switching spectroscopy band-excitation piezoresponse force microscopy, we track the domain wall movement with nanometric spatial precision and analyze the local switching behavior. Phase field simulations show that the reversible long-range motion is intrinsic to the hexagonal manganites, linking it to their improper ferroelectricity and topologically protected structural vortex lines, which serve as anchor point for the ferroelectric domain walls. Our results give new insight into the local dynamics of domain walls in improper ferroelectrics and demonstrate the possibility to reversibly displace domain walls over much larger distances than commonly expected for ferroelectric systems in their pristine state, ensuring predictable device behavior for applications such as tunable capacitors or sensors.

Zahn, Manuel [Norwegian Univ. of Science and Techn↗