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At least 1,225 records · Page 68

Mass enhancement in 3 d and s - p perovskites from symmetry breaking

In some d-electron oxides, the measured effective mass m* exptl has long been known to be significantly larger than the model effective mass m* model deduced from mean-field band theory, i.e., m* exptl =βm* model , where β>1 is the “mass-enhancement” or “mass-renormalization” factor. Previous applications of density functional theory (DFT), based on a symmetry-restricted structure with the smallest number of possible magnetic, orbital, and structural degrees of freedom, missed such mass enhancement. This fact has been taken as evidence of strong electronic correlation, often described via the symmetry-restricted dynamic mean-field approach of the many-body theory, being the exclusive enabling physics. This paper uses instead a static density functional approach that does not restrict positional or spin degrees of freedom (symmetry-broken structures). This approach analyzes the contributions of different symmetry-broken modalities to mass enhancement for a few nominally highly correlated d-electron perovskites as well as the nominally uncorrelated, closed-shell s-p bonding perovskites. It shows that the energy-lowering symmetry-broken spin effects (e.g., nonzero local moment in the paramagnetic phase) and structural effects (e.g., atomic displacement) as described in mean-field DFT already manifest mass enhancement for both electrons and holes in a range of d-electron perovskites SrVO 3 , SrTiO 3 , BaTiO 3 , and LaMnO 3 , as well as p-electron perovskites CsPbI 3 and SrBiO 3 , including both metals (SrVO 3 ) and insulators (the rest). This is revealed only when enlarged unit cells of the same parent global symmetry, which are large enough to allow for symmetry-breaking distortions and concomitant variations in spin order, are explored for their ability to lower the total energy. Positional symmetry breaking that leads to mass enhancement includes octahedral rotation in halide perovskites such as CsPbI 3 , Jahn-Teller-like Q${+}\atop{2}$ distortion in LaMnO 3 , and bond disproportionation in SrBiO 3 , while magnetic symmetry breaking resulting in mass enhancement includes the formation of a distribution of local moments in SrVO3 that averages to zero in the paramagnetic phase. Not all symmetry breaking leads to significant mass enhancement, e.g., the rather small octahedral rotations in the nearly perfectly cubic SrTiO 3 cause negligible mass enhancement, as do the paraelectric displacements in BaTiO 3 . In principle, by ergodicity, the two descriptions, i.e., the symmetry-restricted dynamic approach with a single time-fluctuating magnetic moment and the symmetry-broken mean-field approach with a static distribution of spatially fluctuated local moments, are not mutually exclusive but are a choice of representation and consequently, a choice of computational efficiency. In approximate implementations, the symmetry-broken mean-field approach appears to remove much of what was strong correlation in dynamically correlated symmetry-restricted solutions, leaving smaller (“weak”) residual correlation with respect to the exact solution.

36 MATERIALS SCIENCE↗

Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains

Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes—A. calidoustus and A. implicatus—as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species

59 BASIC BIOLOGICAL SCIENCES↗

A Deep Learning Approach for Detection and Localization of Leaf Anomalies

The detection and localization of possible diseases in crops are usually automated by resorting to supervised deep learning approaches. In this work, we tackle these goals with unsupervised models, by applying three different types of autoencoders to a specific open-source dataset of healthy and unhealthy pepper and cherry leaf images. CAE, CVAE and VQ-VAE autoencoders are deployed to screen unlabeled images of such a dataset, and compared in terms of image reconstruction, anomaly removal, detection and localization. The vector-quantized variational architecture turns out to be the best performing one with respect to all these targets.

Calabro', Davide↗

Nonlinear control of safety factor gradient in tokamaks using spatially variable electron cyclotron current drives

Active control of plasma properties may be necessary to achieve stable operation of next-generation tokamaks over large time scales. Such control algorithms can regulate the plasma properties to avoid the onset of magnetohydrodynamic (MHD) instabilities. For instance, the global and local properties of the safety factor profile are linked to the onset of neoclassical tearing modes (NTMs). This work proposes a model-based control approach for deterring/delaying NTMs through active modulation of one of the safety factor properties - the gradient of the safety factor profile at a particular rational safety factor surface. In particular, a novel control-oriented model for the local safety factor gradient is developed. The nonlinear control model is governed by a nonautonomous ordinary differential equation that accounts for a given rational safety factor surface’s spatial variation over time. Further, to improve the controllability of the spatially evolving parameter, the control model treats ECH&CD positions, along with noninductive powers, as controllable variables. A nonlinear control algorithm based on feedback linearization with optimization is synthesized to achieve the objective of regulating the safety factor gradient around a given target. The proposed algorithm allocates optimal ECH&CD positions, in addition to auxiliary powers, at each time instant as the rational safety factor surface drifts to locations with a low control authority. Stability guarantees of the proposed control law are also discussed in this work. The proposed algorithm is tested for a DIII-D tokamak scenario in nonlinear simulations carried out using the Control Oriented Transport SIMulator (COTSIM). Both fixed and moving ECH&CD cases are studied, and their outcomes are compared. Simulation results demonstrate that enthusiastic regulation of the safety factor gradient can be achieved during the ramp-up and flat-top phases of tokamak operation in both fixed and moving ECH&CD cases. However, real-time updates of ECH&CD positions can prevent the saturation of auxiliary powers.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Charge Transport in Solvated Donor–Acceptor Functionalized Peptoids: Molecular Dynamics and Rate Theory

Scalable solar-energy conversion requires photoactive materials that combine the efficiency of natural photosynthetic systems with the stability and processability needed for practical applications. Achieving reliable charge transport in soft, self-assembled organic materials remains challenging, as structural fluctuations and environmental effects strongly influence charge-transfer (CT) rates. Here, we present a broadly applicable computational framework for evaluating CT rates in the condensed phase, combining Fermi’s golden rule rate theory with inputs from all-atom molecular dynamics (MD) simulations and first-principles electronic-structure calculations. The approach does not rely on system-specific parametrization and is applicable to a wide range of soft and disordered materials. We demonstrate the applicability and usefulness of the framework on redox-active peptoids functionalized with iron–porphyrin (Fe–P) complexes, a bioinspired platform with programmable donor–acceptor units and tunable three-dimensional organization. The calculated CT rates exhibit strong sensitivity to molecular conformation, with variations spanning several orders of magnitude. This dependence is shown to arise from the pronounced variation in diabatic electronic coupling with the relative orientations and separations of the Fe–P complexes across the conformational ensemble. The framework provides a consistent route for connecting atomistic structure to CT kinetics in the condensed phase and enables analysis of structure–rate relations in organic semiconducting systems.

Charge transfer↗

Likelihood-based signal and noise analysis for docking of models into cryo-EM maps

Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding applications in both crystallography and cryo-EM. Indeed, previous crystallographic work on the errors in structural models is directly applicable to likelihood targets in cryo-EM. Likelihood targets in Fourier space are derived here to characterize, based on the comparison of half-maps, the direction- and resolution-dependent variation in the strength of both signal and noise in the data. Because the signal depends on local features, the signal and noise are analysed in local regions of the cryo-EM reconstruction. The likelihood analysis extends to prediction of the signal that will be achieved in any docking calculation for a model of specified quality and completeness. A related calculation generalizes a previous measure of the information gained by making the cryo-EM reconstruction.

59 BASIC BIOLOGICAL SCIENCES↗

Greybox Thermal Parameter Identification of Electric Machine Stators

The parameters of electric machine thermal equivalent circuit networks are difficult to predict due to material and manufacturing uncertainties. In this paper, a Greybox system identification approach is used to identify parameters of electric machine stator lumped parameter thermal networks (LPTNs). LPTNs provide a low order, computationally efficient, dynamic model of temperatures at specific locations. Second and third order LPTN model structures are defined as state space equations with stator thermal parameters to be identified. To test the Greybox electric machine stator thermal system identification, five stator motorette prototypes were constructed with controlled variations in slot fill and slot liner thickness. The variation in the motorette thermal parameters and thermal time constants are detected using the Greybox identification. Special attention is given to the impact of sampling rate and Greybox data record length on parameter estimation accuracy.

33 ADVANCED PROPULSION SYSTEMS↗

Novel Approach to PV Inverter Modeling and Simulation Leveraging Experiments, Learning Based Modeling and Co-Simulation

Photovoltaic (PV) inverter manufacturers use custom, proprietary control approaches and topologies in their inverter design. The proprietary nature of these approaches makes it challenging to share electromagnetic transients (EMT) domain models for system studies. This research work presents an approach to develop EMT models from experimental data. We use novel approach in experimental design, high fidelity data collection, use of learning-based modeling, and co-simulation to reduce the time taken to develop an EMT model for an inverter under test (IUT). We used a 20 kW off-the-shelf grid following PV inverter and subjected the inverter to controlled tests. The tests include voltage and frequency step changes, as well as solar irradiance variations. The recorded high frequency data were used to train a neural network model representing the dynamic behavior of the IUT. The model was subsequently imported into an EMT tool using co-simulation techniques, and thus completing the modeling effort.

black box inverter modeling↗

CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method

Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

59 BASIC BIOLOGICAL SCIENCES↗

SILICON CARBIDE THERMOMETRY USING RAMAN SPECTROSCOPY ON IRRADIATED TRISO PARTICLES

Silicon carbide (SiC) passive thermometry has emerged as a promising post-irradiation examination (PIE) technique for estimating irradiation temperature near the end of irradiation. While dilatometry techniques have been traditionally used to analyze prismatic samples after irradiation, Raman spectroscopy has recently been shown to provide comparable results by analyzing Raman-active phonon modes. In this work, Raman spectroscopy has been applied to the SiC layer of cross-sectioned irradiation tristructural isotropic (TRISO) particles from the AGR-5/6/7 experiment to evaluate the feasibility of particle-scale passive thermometry. Two-dimensional Raman mapping was used to measure the position of the SiC longitudinal optical (LO) phonon, which was then converted to an apparent irradiation temperature using a previously established empirical correlation. Particles from AGR-5/6/7 Compacts 2-2-1 and 5-1-3 were selected as their calculated time-averaged, volume-averaged (TAVA) temperatures (828°C and 706°C, respectively) fall within the range of the sensitivity of the experimental approach. The use of SiC thermometry was anticipated to confirm or highlight potential deviations from calculated end-of-life TAVA temperature across compacts. Four particles from Compact 2-2-1 and two particles from Compact 5-1-3 were selected based on 110mAg inventory (either some measurable activity or below the minimum detection limit) which is commonly used as an indicator of in-pile temperature variation of particles within the same compact. Across every particle selected it was determined that the average LO peak position was located around 968 cm-1 to 969 cm-1. Using the previously determined empirical correlation, this corresponds to an irradiation temperature around 950°C to 966°C, which does not align with the reported TAVA temperature values. This discrepancy in apparent irradiation temperatures likely reflects a combination of uncertainties in the calculated particle temperatures and differences in irradiation history between the present specimens and those used to establish the empirical Raman calibration such as neutron flux (damage rate) and SiC microstructure (as fabricated and irradiated).

Vawdrey, Josh [ORNL]↗

Anharmonic multi-phonon nonradiative transition: An ab initio calculation approach

Nonradiative carrier recombinations at deep centers in semiconductors are of great importance for both fundamental physics and device engineering. Here, we provide a revised analysis of Huang’s original nonradiative multi-phonon (NMP) theory with ab initio calculations. First, we confirmed at the first-principles level that Huang’s concise formula gives the same results as the matrix-based formula, and that Huang’s high-temperature formula provides an analytical expression for the coupling constant in Marcus theory. Secondly, we correct for anharmonic effects by taking into account local phonon-mode variations for different charge states of a defect. The corrected capture rates for defects in GaN and SiC agree well with experiments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A Self-learning Neural Network Approach for Radio Frequency Interference Detection and Removal in Radio Astronomy

In this work, we present a novel neural network (NN) method for the detection and removal of radio frequency interference (RFI) from the raw digitized signal in the signal processing chain of a typical radio astronomy experiment. The main advantage of our method is that it does not require a training set. Instead, our method relies on the fact that the true signal of interest coming from astronomical sources is thermal and therefore described as a Gaussian random process, which cannot be compressed. We employ a variational encoder/decoder network to find the compressible information in the data stream that can explain the most variance with the fewest degrees of freedom. We demonstrate it on a set of toy problems and stored ring buffers from the Baryon Mapping eXperiment prototype. We find that the RFI subtraction is effective at cleaning simulated time streams: While we find that the power spectra of the RFI-cleaned time streams output by the NN suffer from extra signal consistent with additive noise, we find that it is generally around percent level across the band and sub 10% in contaminated spectral channels even when RFI power is an order of magnitude larger than the signal. We discuss the advantages and limitations of this method and possible implementation in the front end of future radio experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

Unsteady aerodynamics of large-scale floating offshore wind turbines in surge motion

Unsteady aerodynamic loads significantly influence the design and wake flow field of floating offshore wind turbines, especially due to wave- or vibration-induced tower top motions triggering various unsteady phenomena. Recent studies show that increasing turbine sizes amplify unsteady aerodynamic effects, as their impact typically grows with rotor diameter. This work combines recent findings from experiments and simulations on model-scale FOWT aerodynamics with new numerical analyses of large-scale rotors, providing a comprehensive understanding of unsteady phenomena occurrence and impact. Numerical analyses of the IEA 15-MW and 22-MW rotors undergoing surge motions characterise the combined influence of motion-induced unsteady phenomena on rotor thrust. Results indicate that unsteady effects can reduce thrust force variations by up to 40% at realistic surge periods. These findings contrast with prior model-scale rotor investigations, attributed to the specialised design of the model rotors. Comparisons between numerical methods - the dynamic blade element momentum method in OpenFAST and free vortex wake modules in panMARE and OpenFAST - reveal persistent differences in thrust predictions under both idealised and realistic conditions. This highlights that classical blade element momentum approaches require enhancement to accurately capture unsteady loads on large-scale floating offshore wind turbines at low wind speeds.

16 TIDAL AND WAVE POWER↗

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii

Abstract Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.

59 BASIC BIOLOGICAL SCIENCES↗

Cheaper and more noise-resilient quantum state preparation using eigenvector continuation

Subspace methods are powerful, noise-resilient methods that can effectively prepare ground states on quantum computers. The challenge is to get a subspace with a small condition number that spans the states of interest using minimal quantum resources. In this work, we will use eigenvector continuation to build a subspace from the low-lying states of a set of Hamiltonians. The basis vectors are prepared using truncated versions of standard state preparation methods such as imaginary-time evolution (ITE), adiabatic state preparation (ASP), and variational quantum eigensolver. By using these truncated methods combined with eigenvector continuation, we can directly improve upon them, obtaining more accurate ground-state energies at a reduced cost. We use several spin systems to demonstrate convergence even when methods like ITE and ASP fail, such as ASP in the presence of level crossings and ITE with vanishing energy gaps. We also showcase the noise resilience of this approach beyond the gains already made by having shallower quantum circuits. Furthermore, our findings suggest that eigenvector continuation can be used to improve existing state preparation methods in the near term.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Assessment of Microstructure Prediction Capabilities for Powder Bed Fusion Stainless Steel 316

The Advanced Materials and Manufacturing Technologies program aims to accelerate the development, qualification, demonstration, and deployment of advanced materials and manufacturing technologies to enable reliable and economical nuclear energy. However, the characteristic process-structure-property relationships of additive manufacturing (AM) materials pose challenges for the qualification and certification of AM nuclear components. In particular, component-scale variations in microstructure and properties can be driven by localized changes in melt pool dynamics due to how process parameters interact with different part geometries. Computational modeling tools can play a crucial role in predicting and controlling this variability. This report presents final results on process modeling tools designed to predict microstructure variability in additively manufactured stainless steel 316 parts. It details the software packages and physical modeling approaches employed to simulate an AM component within an automated process modeling workflow. Results are demonstrated through comparisons between predicted microstructures and experimental measurements across various representative processing conditions. The report concludes by discussing identified challenges and future opportunities for connecting the developed simulation workflow with mechanics simulations for prediction of part performance.

36 MATERIALS SCIENCE↗

Diagnosing Malaria Patients with Plasmodium falciparum and vivax Using Deep Learning for Thick Smear Images

We propose a new framework, PlasmodiumVF-Net, to analyze thick smear microscopy images for a malaria diagnosis on both image and patient-level. Our framework detects whether a patient is infected, and in case of a malarial infection, reports whether the patient is infected by Plasmodium falciparum or Plasmodium vivax. PlasmodiumVF-Net first detects candidates for Plasmodium parasites using a Mask Regional-Convolutional Neural Network (Mask R-CNN), filters out false positives using a ResNet50 classifier, and then follows a new approach to recognize parasite species based on a score obtained from the number of detected patches and their aggregated probabilities for all of the patient images. Reporting a patient-level decision is highly challenging, and therefore reported less often in the literature, due to the small size of detected parasites, the similarity to staining artifacts, the similarity of species in different development stages, and illumination or color variations on patient-level. We use a manually annotated dataset consisting of 350 patients, with about 6000 images, which we make publicly available together with this manuscript. Our framework achieves an overall accuracy above 90% on image and patient-level.

60 APPLIED LIFE SCIENCES↗

Assessing the climate impact of an improved volcanic sulfate aerosol representation in E3SM

Accurately simulating historical surface temperature variations is essential for evaluating climate models, yet many struggle to reproduce the mid-20th-century temperature trends associated with significant volcanic eruptions. This study examines the impact of volcanic sulfate aerosol representation on these biases using the Energy Exascale Earth System Model (E3SM). The standard CMIP6 protocol prescribes volcanic forcing through radiative perturbations, omitting volcanic aerosol–cloud interactions (VACIs). Here, we implement an emission-based approach with an updated volcanic eruption inventory that directly incorporates volcanic sulfur dioxide (SO 2 ) emissions, enabling a more process-based representation of volcanic forcing. This approach leads to improved surface temperature variability and a modest reduction in cold biases between 1940 and 1980 compared to the CMIP6 setup. Additionally, we assess cloud property responses to a more realistic volcanic sulfate aerosol representation, which weakens cloud-induced cooling during periods of lower volcanic activity. However, despite these refinements, a significant temperature cold bias remains, indicating that further improvements in atmospheric chemistry, aerosol microphysics, cloud processes, and model parameterizations are needed to fully resolve this issue in E3SM.

54 ENVIRONMENTAL SCIENCES↗