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At least 613 records · Page 34

Fast and Accurate Predictions of Total Energy for Solid Solution Alloys with Graph Convolutional Neural Networks

We use graph convolutional neural networks (GCNNs) to produce fast and accurate predictions of the total energy of solid solution binary alloys. GCNNs allow us to abstract the lattice structure of a solid material as a graph, whereby atoms are modeled as nodes and metallic bonds as edges. This representation naturally incorporates information about the structure of the material, thereby eliminating the need for computationally expensive data pre-processing which would be required with standard neural network (NN) approaches. We train GCNNs on ab-initio density functional theory (DFT) for copper-gold (CuAu) and iron-platinum (FePt) data that has been generated by running the LSMS-3 code, which implements a locally self-consistent multiple scattering method, on OLCF supercomputers Titan and Summit. GCNN outperforms the ab-initio DFT simulation by orders of magnitude in terms of computational time to produce the estimate of the total energy for a given atomic configuration of the lattice structure. We compare the predictive performance of GCNN models against a standard NN such as dense feedforward multi-layer perceptron (MLP) by using the root-mean-squared errors to quantify the predictive quality of the deep learning (DL) models. We find that the attainable accuracy of GCNNs is at least an order of magnitude better than that of the MLP.

Lupo Pasini, Massimiliano↗

AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.

60 APPLIED LIFE SCIENCES↗

Defect-mediated selective hydrogenation of nitroarenes on nanostructured WS 2

Transition metal dichalcogenides (TMDs) are well known catalysts as both bulk and nanoscale materials. Two-dimensional (2-D) TMDs, which contain single- and few-layer nanosheets, are increasingly studied as catalytic materials because of their unique thickness-dependent properties and high surface areas. Here, colloidal 2H-WS 2 nanostructures are used as a model 2-D TMD system to understand how high catalytic activity and selectivity can be achieved for useful organic transformations. Free-standing, colloidal 2H-WS 2 nanostructures containing few-layer nanosheets are shown to catalyze the selective hydrogenation of a broad scope of substituted nitroarenes to their corresponding aniline derivatives in the presence of other reducible functional groups. Microscopic and computational studies reveal the important roles of sulfur vacancy-rich basal planes and tungsten-terminated edges, which are more abundant in nanostructured 2-D materials than in their bulk counterparts, in enabling the functional group selectivity. At tungsten-terminated edges and on regions of the basal planes having high concentrations of sulfur vacancies, vertical adsorption of the nitroarene is favored, thus facilitating hydrogen transfer exclusively to the nitro group due to geometric effects. At lower sulfur vacancy concentrations on the basal planes, parallel adsorption of the nitroarene is favored, and the nitro group is selectively hydrogenated due to a lower kinetic barrier. These mechanistic insights reveal how the various defect structures and configurations on 2-D TMD nanostructures facilitate functional group selectivity through distinct mechanisms that depend upon the adsorption geometry, which may have important implications for the design of new and enhanced 2-D catalytic materials across a potentially broad scope of reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental studies of plasma-antenna coupling with the JET Alfvén Eigenmode Active Diagnostic

Here, this paper presents a dedicated study of plasma-antenna (PA) coupling with the Alfvén Eigenmode Active Diagnostic (AEAD) in JET. Stable AEs and their resonant frequencies f, damping rates γ < 0, and toroidal mode numbers n are measured for various PA separations and limiter versus X-point magnetic configurations. Two stable AEs are observed to be resonantly excited at distinct low and high frequencies in limiter plasmas. The values of f and n do not vary with PA separation. However, |γ| increases with PA separation for the low-f, but not high-f, mode, yet this may be due to slightly different edge conditions. The high-f AE is detected throughout the transition from limiter to X-point configuration, though its damping rate increases; the low-f mode, on the other hand, becomes unidentifiable. The linear, resistive MHD code CASTOR is used to simulate the frequency scan of an AEAD-like external antenna. For the limiter pulses, the high-f mode is determined to be an n = 0 GAE, while the low-f mode is likely an n = 2 TAE. During the transition from limiter to X-point configuration, CASTOR indicates that n = 1 and 2 EAEs are excited in the edge gap. These results extend previous experimental studies in JET and Alcator C-Mod; validate the computational work performed by Dvornova et al; and provide guidance for the optimization of PA coupling in upcoming JET energetic particle experiments, for which the AEAD will aim to identify the contribution of alpha particles to AE drive during the DT campaign.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dynamics of threading dislocations in porous heteroepitaxial GaN films

Behavior of threading dislocations in porous heteroepitaxial gallium nitride (GaN) films has been studied using computer simulation by the two-dimensional discrete dislocation dynamics approach. A computational scheme, where pores are modeled as cross sections of cylindrical cavities, elastically interacting with unidirectional parallel edge dislocations, which imitate threading dislocations, is used. Time dependences of coordinates and velocities of each dislocation from dislocation ensembles under investigation are obtained. Visualization of current structure of dislocation ensemble is performed in the form of a location map of dislocations at any time. It has been shown that the density of appearing dislocation structures significantly depends on the ratio of area of a pore cross section to area of the simulation region. In particular, increasing the portion of pores surface on the layer surface up to 2% should lead to about a 1.5-times decrease of the final density of threading dislocations, and increase of this portion up to 15% should lead to approximately a 4.5-times decrease of it.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

2025 Atmospheric Radiation Measurement (ARM) Annual Report

ARM is a multi-laboratory, U.S. Department of Energy (DOE) Office of Science user facility and a key contributor to atmospheric research efforts. For more than 30 years, ARM has supported the DOE and Office of Science missions by providing atmospheric observations to enable scientific discovery, transform our understanding of the atmosphere, and evaluate and improve the accuracy of atmospheric models. ARM’s cutting-edge capabilities for scientists include continuously operating ground-based observatories, aerial observation platforms, and high performance computing.

54 ENVIRONMENTAL SCIENCES↗

Experimental studies of plasma-antenna coupling with the JET Alfven Eigenmode Active Diagnostic

This paper presents a dedicated study of plasma-antenna (PA) coupling with the Alfven Eigenmode Active Diagnostic (AEAD) in JET. Stable AEs and their resonant frequencies f, damping rates gamma < 0, and toroidal mode numbers n are measured for various PA separations and limiter versus X-point magnetic configurations. Two stable AEs are observed to be resonantly excited at distinct low and high frequencies in limiter plasmas. The values of f and n do not vary with PA separation. However, |gamma| increases with PA separation for the low-f, but not high-f, mode, yet this may be due to slightly different edge conditions. The high-f AE is detected throughout the transition from limiter to X-point configuration, though its damping rate increases; the low-f mode, on the other hand, becomes unidentifiable. The linear resistive MHD code CASTOR is used to simulate the frequency scan of an AEAD-like external antenna. For the limiter pulses, the high-f mode is determined to be an n = 0 GAE, while the low-f mode is likely an n = 2 TAE. During the transition from limiter to X-point configuration, CASTOR indicates that n = 1 and 2 EAEs are excited in the edge gap. These results extend previous experimental studies in JET and Alcator C-Mod; validate the computational work performed by Dvornova et al 2020 Phys. Plasmas 27 012507; and provide guidance for the optimization of PA coupling in upcoming JET energetic particle experiments, for which the AEAD will aim to identify the contribution of alpha particles to AE drive during the DT campaign.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗

Characterisation of two-stage ignition in diesel engine-relevant thermochemical conditions using direct numerical simulation

With the goal of providing a more detailed fundamental understanding of ignition processes in diesel engines, this study reports analysis of a direct numerical simulation (DNS) database. In the DNS, a pseudo turbulent mixing layer of dimethyl ether (DME) at 400 K and air at 900 K is simulated at a pressure of 40 atmospheres. At these conditions, DME exhibits a two-stage ignition and resides within the negative temperature coefficient (NTC) regime of ignition delay times, similar to diesel fuel. The analysis reveals a complex ignition process with several novel features. Autoignition occurs as a distributed, two-stage event. The high-temperature stage of ignition establishes edge flames that have a hybrid premixed/autoignition flame structure similar to that previously observed for lifted laminar flames at similar thermochemical conditions. In conclusion, a combustion mode analysis based on key radical species illustrates the multi-stage and multi-mode nature of the ignition process and highlights the substantial modelling challenge presented by diesel combustion.

33 ADVANCED PROPULSION SYSTEMS↗

Partnership Center for High-Fidelity Boundary Plasma Simulation (Final Report)

Within the Partnership Center for High-Fidelity Boundary Plasma Simulation (HBPS), work at UT-Austin was aimed at improved verification, validation, and uncertainty quantification (VVUQ) for edge plasma simulations and on performing gyrokinetics simulations of pedestal instabilities and turbulence in order to expand foundational understanding of pedestal transport. Regarding VVUQ, the accomplishments can be summarized as follows. First, it was shown that the Moment Preserving Constrained Resampling technique, when applied periodically in particle-in-cell simulations in the XGC code, can dramatically improve the accuracy of the simulation at essentially equivalent computational cost. Second, a technique for estimating model correlations, which are required to solve the model selection and sample allocation problem in multifidelity UQ techniques, without sampling the highest fidelity, most computationally expensive model, was developed and demonstrated. Third, previously developed methods for estimating statistical and discretization errors were applied to numerical methods relevant to edge plasma simulations, namely in particle-in-cell-based approaches, and shown to work. Finally, benchmark studies for comparing gyrokinetic codes were developed and performed, leading to reasonable agreement between four commonly used codes. Regarding physics studies, gyrokinetic simulations to investigate microtearing modes in the DIII-D pedestal were performed using the GENE code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Portable Parallel Algorithms and Frameworks for Exascale Graph Analytics

Graphs (or networks) are a tool used to model the interactions among various entities. Efficiently processing large graphs has recently attracted significant attention due to the applications of graphs in various domains, such as biology, chemistry, and cyber-security. Analyzing the structure and properties of these graphs is an important component of many scientific computing pipelines. With the explosion in the volume of data, graphs have become very large and can contain hundreds of billions of vertices and trillions of edges. Therefore, it is crucial to develop high-performance methods to enable graph analysis to be done quickly and energy-efficiently. Furthermore, these solutions should be highly parallel in order to take advantage of modern parallel machines. However, designing efficient solutions is not enough. With the wide variety of computing environments available, each with different programmability and performance characteristics, it is necessary to develop solutions that are portable in terms of both performance (i.e., provide theoretical guarantees) and programmability (i.e., provide high level abstractions).

97 MATHEMATICS AND COMPUTING↗

A BOUT++ extension for full annular tokamak edge MHD and turbulence simulations

For tokamak edge plasma simulation, a plasma simulation framework BOUT++ employs a dual coordinate system to simulate moderate-n and high-n plasma instability with reasonable computational cost, where n is the toroidal mode number. This coordinate system however limits the computational domain to the toroidal wedge (full torus divided into N parts in the toroidal direction) for computational efficiency and the use of flute-ordering approximation in the field solver calculating the flow potential from the vorticity which may not be valid for low-n modes. Improving numerical treatment of low-n modes is however indispensable to address simulations of low-n current-driven edge localized mode (ELM), ELM control by resonant magnetic perturbations (RMPs), edge turbulence with RMPs and so on. In this work, BOUT++ is extended to simulate the interplay between $n=0$, low-n and high-n plasma components in a full annular tokamak edge domain through hybrid modeling of the flow potential and the vorticity. Low-n modes of flow potential are calculated in an orthogonal flux surface coordinate and high-n modes in the dual coordinate system separately in Fourier space. Finally, the proposed scheme can capture an interplay between $n=1$ global modes and high-n turbulence during pedestal collapse in a full annular torus domain with a circular cross section.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

MARS-F/K modeling of plasma response and fast ion losses due to RMP in KSTAR

Abstract The toroidal single-fluid magnetohydrodynamic (MHD) code MARS-F (Liu et al 2000 Phys. Plasmas 7 3681) and the MHD-kinetic hybrid code MARS-K (Liu et al 2008 Phys. Plasmas 15 112503) are utilized to study the plasma response to the n = 1 ( n is the toroidal mode number) resonant magnetic perturbation (RMP), applied to suppress the type-I edge localized mode (ELM) in a KSTAR discharge. Both the resistive-rotating and ideal-static plasma models identify strong screening of the resonant radial field harmonics of the applied RMP due to the plasma response, and predict a strong edge-peeling response of the plasma which is consistent with the optimal ELM control coil current configuration adopted in experiment. The RMP-induced radial displacement of the plasma, computed by the resistive-rotating plasma model, agrees reasonably well with that reconstructed from the measured data in the plasma core. Taking into account the drift kinetic response of fast ions, MARS-K hybrid modeling also finds quantitative agreement of the plasma core fluid pressure perturbation with experiment. Based on the MARS-F computed plasma response, a guiding-center orbit-tracing simulation finds about 0.3% of fast ion losses due the n = 1 RMP in the KSTAR ELM control experiment considered. Most losses are associated with counter-current fast ions located near the plasma edge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

OmniXAS: A universal deep-learning framework for materials x-ray absorption spectra

X-ray absorption spectroscopy (XAS) is a powerful characterization technique for probing the local chemical environment of absorbing atoms. However, analyzing XAS data presents significant challenges, often requiring extensive, computationally intensive simulations, as well as significant domain expertise. These limitations hinder the development of fast, robust XAS analysis pipelines that are essential in high-throughput studies and for autonomous experimentation. Here, we address these challenges with OmniXAS, a framework that contains a suite of transfer learning approaches for XAS prediction, each uniquely contributing to improved accuracy and efficiency, as demonstrated on the K-edge spectra database covering eight 3⁢d transition metals (Ti–Cu). The OmniXAS framework is built upon three distinct strategies. First, we use M3GNet [Nat. Comput. Sci. 2, 718 (2022)] to derive latent representations of the local chemical environment of absorption sites as input for XAS prediction, achieving significant improvements over conventional featurization techniques. Second, we employ a hierarchical transfer learning strategy, training a universal multitask model across elements before fine-tuning for element-specific predictions. Models based on this cascaded approach after elementwise fine-tuning outperform element-specific models by up to 69%. Third, we implement cross-fidelity transfer learning, adapting a universal model to predict spectra generated by simulation of a different fidelity with a much higher computational cost. This approach improves prediction accuracy by up to 11% over models trained on the target fidelity alone. Our approach significantly boosts the throughput of XAS modeling by orders of magnitude as compared to first-principles simulations and is extendable to XAS prediction for a broader range of elements. The proposed transfer learning framework is generalizable to enhance deep-learning models that target other properties in materials research.

36 MATERIALS SCIENCE↗

Diffraction of radio frequency waves by spatially modulated interfaces in the plasma edge in tokamaks

We report the use of radio frequency (RF) waves in fusion plasmas for heating, for non-inductive current generation, for profile control and for diagnostics has been well established. The RF waves, excited by antenna structures placed near the wall of a fusion device, have to propagate through density fluctuations at the plasma edge. These fluctuations can modify the properties of the RF waves that propagate towards the core of the plasma. A full-wave electromagnetic computational code ScaRF based on the finite difference frequency domain (FDFD) method has been developed to study the effect of density turbulence on RF waves. The anisotropic plasma permittivity used in the scattering studies is that for a magnetized, cold plasma. The code is used to study the propagation of an RF plane wave through a modulated, spatially periodic density interface. Such an interface could arise in the edge region due to magnetohydrodynamic instability or drift waves. The frequency of the plane wave is taken to be in the range of the electron cyclotron frequency. The scattering analysis is applicable to ITER-like plasmas, as well as to plasmas in medium sized tokamaks such as TCV, ASDEX-U and DIII-D. The effect of different density contrasts across the interface and of different spatial modulations are discussed. While ScaRF is used to study a periodic density fluctuation, the code is general enough to include different varieties of density fluctuations in the edge region – such as blobs and filaments, and spatially random fluctuations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Diffraction of radio frequency waves by spatially modulated interfaces in the plasma edge in tokamaks

The use of radio frequency (RF) waves in fusion plasmas for heating, for non-inductive current generation, for profile control, and for diagnostics has been well established. The RF waves, excited by antenna structures placed near the wall of a fusion device, have to propagate through density fluctuations in the plasma edge. These fluctuations can modify the properties of the RF waves that propagate towards the core of the plasma. A full-wave electromagnetic computational code ScaRF based on the finite diifference frequency domain (FDFD) method has been developed to study the effect of density turbulence on RF waves. The anisotropic plasma permittivity used in the scattering studies is that for a magnetized, cold plasma. The code is used to study the propagation of an RF plane wave through a modulated, spatially periodic density interface. Such an interface could arise in the edge region due to magnetohydrodynamic instability or drift waves. The frequency of the plane wave is taken to be in the range of the electron cyclotron frequency. The scattering analysis is applicable to ITER-like plasmas, as well as to plasmas in medium sized tokamaks such as TCV, ASDEX-U, and DIII-D. The effect of diifferent density contrasts across the interface and of diifferent spatial modulations are discussed. While ScaRF is used to study a periodic density fluctuation, the code is general enough to include diifferent varieties of density fluctuations in the edge region -- such as blobs and filaments, and spatially random fluctuations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Defect Structure in Quantum-Cutting Yb3+-Doped CsPbCl3 Perovskites Probed by X-Ray Absorption and Atomic Pair Distribution Function Analysis

Ytterbium-doping in all-inorganic lead-halide perovskites (CsPb(Cl1-xBrx)3) generates novel properties including quantum cutting and narrow line emission, making these materials attractive spectral down-converters for solar photovoltaics. The relationship between this optical efficiency and the defect structure(s) associated with Yb3+ dopants within perovskites is not well understood. Various charge-neutral doping motifs have previously been proposed and studied computationally, including clusters involving two substitutional Yb3+ ions charge-compensated by a single local Pb2+ vacancy. Near-band-edge defect states associated with such motifs are believed to play an important mechanistic role in quantum cutting itself. Here, we report the results of X-ray absorption and X-ray total-scattering measurements on ytterbium-doped CsPbCl3. XANES shows that the dopant oxidation state is exclusively Yb3+, and a combination of Yb L3 and Pb L3 EXAFS shows that this Yb3+ substitutes exclusively at Pb2+ sites, where it adopts a pseudo-octahedral [YbCl6]3- coordination environment. Shell-by-shell fits to the data show a short Yb-Cl bond distance of 2.58 Å compared to the Pb-Cl bond distance of 2.83 Å. We confirm this finding by X-ray pair distribution function analysis, which also shows evidence of additional Pb2+ vacancy formation induced by Yb3+ doping. We evaluate whether this is the primary mechanism of charge compensation using simulated EXAFS and pair distribution function data for several computed defect structures. Together, these results resolve the local dopant structures and charge-compensation mechanisms in lanthanide-doped all-inorganic lead-halide perovskites, and, as such, significantly advance the understanding of structure-function relationships in this important class of materials.

Kluherz, Kyle (ORCID:0000000279865167)↗

A Medium-/Low-Voltage Joint State Estimator Through Linear Uncertainty Propagation

Traditionally, distribution system state estimations (DSSE) are challenged by the lack of measurements at both primary and secondary sides of the system. The widely available cable television (CATV) voltage sensors installed in low-voltage (LV) networks bring opportunities to achieve higher quality DSSE covering a broader area of the distribution network. This study proposes a medium-/low-voltage (MV/LV) joint distribution system state estimation approach using the untapped CATV measurements. It aims at addressing the need for system situational awareness at the grid edge while improving the estimation accuracy at both the primary and secondary sides compared to its disjointed counterpart. Linearized measurement functions and boundary condition uncertainty propagation rules are derived to ensure the computational efficiency and accuracy of the joint state estimator. Numerical experiments are conducted on an IEEE test feeder to demonstrate the efficacy of the proposed method and the value of CATV measurements.

joint state estimation↗