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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,171 records · Page 65

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perspectives on the relationship between materials chemistry and roll-to-roll electrode manufacturing for high-energy lithium-ion batteries

As lithium-ion battery (LIB) active material and cell manufacturing costs continue to drop with wider adoption of electric vehicles, electrode and cell processing costs remain too high in terms of reaching the ultimate U.S. Department of Energy (DOE) cell cost target of $80/kWh. This paper primarily covers major materials chemistry advancements made over the last 10 years at Oak Ridge National Laboratory (ORNL) in the space of advanced manufacturing science for LIBs with the aim of simultaneously meeting the ultimate cost target, 500 Wh/kg gravimetric energy density, 10-15-min fast charge times, and 1000 deep discharge cycles. Aqeous electrode processing with a variety of active anode and cathode materials is now a standard procedure at the DOE Battery Manufacturing R&D Facility at ORNL (BMF), including the latest processes developed for Ni-rich cathodes. New results on cobalt-free LiNi 0.8 Fe 0.1 Al 0.1 O 2 (NFA 811) are also included and discussed in an electrode processing advantage context. In addition, colloidal processing advancements have been made for Si/C composite anodes for achieving >600 mA h/g capacities. Optimization of electrode coating parameters and drying protocols have been completed, which has elucidated how key processing variables need to be changed when parameters such as slurry solids loading, solvent type, and wet electrode thickness are changed. ORNL has also increased the line speeds at which thick cathodes can be processed using ultra-fast electron beam (EB) curing and substantially decreased formation cycling times to <1 day. Finally, key details of these advancements are discussed in the context of materials chemistry and process-property-performance relationships.

25 ENERGY STORAGE↗

Dynamics of the spatial scale of visual attention revealed by brain event-related potentials

The temporal dynamics of the spatial scaling of attention during visual search were examined by recording event-related potentials (ERPs). A total of 16 young participants performed a search task in which the search array was preceded by valid cues that varied in size and hence in precision of target localization. The effects of cue size on short-latency (P1 and N1) ERP components, and the time course of these effects with variation in cue-target stimulus onset asynchrony (SOA), were examined. Reaction time (RT) to discriminate a target was prolonged as cue size increased. The amplitudes of the posterior P1 and N1 components of the ERP evoked by the search array were affected in opposite ways by the size of the precue: P1 amplitude increased whereas N1 amplitude decreased as cue size increased, particularly following the shortest SOA. The results show that when top-down information about the region to be searched is less precise (larger cues), RT is slowed and the neural generators of P1 become more active, reflecting the additional computations required in changing the spatial scale of attention to the appropriate element size to facilitate target discrimination. In contrast, the decrease in N1 amplitude with cue size may reflect a broadening of the spatial gradient of attention. The results provide electrophysiological evidence that changes in the spatial scale of attention modulate neural activity in early visual cortical areas and activate at least two temporally overlapping component processes during visual search.

Non-NASA Center↗

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

The COVID-19 disease caused by the SARS-CoV-2 coronavirus has become a pandemic health crisis. An attractive target for antiviral inhibitors is the main protease 3CL Mpro due to its essential role in processing the polyproteins translated from viral RNA. Here we report the room temperature X-ray structure of unliganded SARS-CoV-2 3CL Mpro, revealing the ligand-free structure of the active site and the conformation of the catalytic site cavity at near-physiological temperature. Comparison with previously reported low-temperature ligand-free and inhibitor-bound structures suggest that the room temperature structure may provide more relevant information at physiological temperatures for aiding in molecular docking studies.

59 BASIC BIOLOGICAL SCIENCES↗

Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines

Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of the SARS-CoV -2 proteome in three dimensions (3D) during the first 6 months of the COVID -19 pandemic

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Here detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Targeting transcription factors through an IMiD independent zinc finger domain

Abstract Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.

Liu, Bee Hui↗

Heterogeneous Outgassing Regions Identified on Active Centaur 29P/Schwassmann–Wachmann 1

Centaurs are transitional objects between primitive trans-Neptunian objects and Jupiter-family comets. Their compositions and activities provide fundamental clues regarding the processes affecting the evolution of and interplay between these small bodies. Here we report observations of centaur 29P/Schwassmann–Wachmann 1 (29P) with the James Webb Space Telescope (JWST). We identified localized jets with heterogeneous compositions driving the outgassing activity. We employed the NIRSpec mapping spectrometer to study the fluorescence emissions of CO and obtain a definitive detection of CO 2 for this target. The exquisite sensitivity of the instrument also enabled carbon and oxygen isotopic signatures to be probed. Molecular maps reveal complex outgassing distributions, such as jets and anisotropic morphology, which indicate that 29P’s nucleus is dominated by active regions with heterogeneous compositions. These distributions could reflect that it has a bilobate structure with compositionally distinct components or that strong differential erosion takes place on the nucleus. As there are no missions currently planning to visit a centaur, these observations demonstrate JWST’s unique capabilities in characterizing these objects.

Sara Faggi↗

The development of the DAST I remotely piloted research vehicle for flight testing an active flutter suppression control system

The development of the DAST I (drones for aerodynamic and structural testing) remotely piloted research vehicle is described. The DAST I is a highly modified BQM-34E/F Firebee II Supersonic Aerial Target incorporating a swept supercritical wing designed to flutter within the vehicle's flight envelope. The predicted flutter and rigid body characteristics are presented. A description of the analysis and design of an active flutter suppression control system (FSS) designed to increase the flutter boundary of the DAST wing (ARW-1) by a factor of 20% is given. The design and development of the digital remotely augmented primary flight control system and on-board analog backup control system is presented. An evaluation of the near real-time flight flutter testing methods is made by comparing results of five flutter testing techniques on simulated DAST I flutter data. The development of the DAST ARW-1 state variable model used to generate time histories of simulated accelerometer responses is presented. This model uses control surface commands and a Dryden model gust as inputs. The feasibility of the concept of extracting open loop flutter characteristics from closed loop FSS responses was examined. It was shown that open loop characteristics can be determined very well from closed loop subcritical responses.

Grose, D. L.↗

On the Hunt for Detectable Biosignatures in Jezero Crater: What to Look for and Where

Introduction: The Perseverance rover, which is currently exploring Jezero crater on Mars, is equipped with seven instruments that allow for observation of textures, minerals, color, structure, and chemistry of rocks and sediments in order to search for signs of ancient life, understand the geologic history of the crater, and identify candidates for sample return (Farley et al. 2020). The first of these aims includes the direct detection of potential biosignatures, including textures, organic molecules, minerals, and elemental chemistries that are of biogenic origin (Mustard et al. 2013). The presence of these biosignatures will be constrained by the habitability of the local region, the preservation potential of the host rocks, and the sensitivity of the instrument suite, and their biogenicity will be investigated after return to Earth as part of the Mars Sample Return campaign. Here, we examine key targets on the three planned campaigns, potential biosignatures that may be present, and the capabilities of key rover instruments. High Potential Biosignature Sites in Jezero: To date, measurements have been made on multiple sites that both contain minerals known in terrestrial settings to preserve biosignatures and likely were habitable settings (Williford et al. 2021). Two examples include the fine-grained rocks at the base of the delta fan and the NW inner margin of the crater. Fine-grained Rocks at Base of Delta Fan. Fine-grained, clay-bearing rocks may have been deposited as muddy lake sediments that could have hosted life and preserved biosignatures settling out of the water column. The report of organic molecules by the Curiosity rover in the Sheepbed mudstone and Murray formation has highlighted this site in particular. Potential biosignatures in mudstones, especially those rich in silica (McMahon et al. 2018), microbialites and complex organics. NW Inner Margin of Crater. This unit, located along the inner margin of the crater, contains strong carbonate signatures and may have been the littoral zone of a lake (Horgan et al. 2020). The potential biosignatures here include microfossils, microbialites, biominerals, and complex organics. Detectability of Biosignatures by the Mars 2020 Instrument Suite: The Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument comprises a Deep UV spectrometer, context imager, and color camera to generate spatially resolved chemical maps (Bhartia et al. 2020). It is sensitive to trace organics as well as a range of minerals and can detect native fluorescence from aromatic organics; the WATSON and ACI cameras can be used to observe morphologies such as stromatolitic laminations or filaments ranging from the tens of micron to millimeter scale. SHERLOC can detect organics that may be present in either of the high potential biosignature targets, as well as detect carbonates in the latter. However, the presence of high amounts of iron, such as in iron-rich clays, would cause attenuation of spectral response through UV absorption. The Planetary Instrument for X-ray Lithochemistry (PIXL) comprises an X-ray fluorescence spectrometer and camera that can scan rock surfaces to generate elemental maps (Allwood et al. 2020). PIXL can detect chemical biosignatures such as spatial variations of elemental abundances that may have resulted from biological activity. PIXL would be particularly useful in detecting fine textures and elemental chemistries in either high potential biosignature target, but cannot directly detect minerals such as carbonate. The SuperCam instrument performs three types of spectroscopy, color imaging, and acoustic recording to remotely examine elemental composition, minerals, organics, and textures (Maurice et al. 2021). Using laser induced breakdown spectroscopy and time resolved luminescence spectroscopy, SuperCam can detect major elemental building blocks of organics (i.e., C, H, N, O, P, S) and conjugated organic structures, respectively, which may be found in either site. While in other contexts, luminescence is a useful tool for biosignature identification, luminescence generated by the 532 nm laser may obscure the Raman signal. Conclusion: The three instruments discussed can be used collaboratively to establish the presence of potential biosignatures in samples. These high-priority samples may then be returned to Earth for detailed laboratory analysis.

S. Sharma↗

The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi

Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein–encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain ?cre-1, while glucose repression was still mostly functional in ?exo-1. Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in ?exo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in ?exo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.

Gabriel, Raphael↗

Improved titanium-44 purification process for establishing a high apparent molar activity titanium-44/scandium-44 generator

44 Sc-radiopharmaceuticals are gaining more interest but still lack availability. The proof of principle of a 44 Ti/ 44 Sc generator, which can produce 44 Sc daily, has been established but with some limitations and drawbacks. Despite recent advances, separation of 44 Ti from massive quantities of scandium target material is still cumbersome. Here, in this work, the improved radiochemical separation of 44 Ti from residual scandium target material was carried out by precipitation of Sc with fluoride ions. Furthermore, two approaches were used to set up a high apparent molar activity small-scale generator. The first method relied on extraction chromatography for fine purification using a DGA resin, followed by loading of the purified 44 Ti onto a ZR resin column. In the second method, 44 Ti was loaded on the ZR resin directly after the precipitation step. This second method was used to set up a generator of 370 kBq and evaluate by radiolabeling. An apparent molar activity of 2 MBq/nmol was obtained for the radiolabeling with DOTA, the most common and suitable chelate for scandium. This result is comparable with previously published data on 44m/44 Sc.

44Sc↗

The molecular basis of Human FN3K mediated phosphorylation of glycated substrates

Abstract Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of the target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However, the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in the apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rational small molecule design targeting FN3K.

Science & Technology - Other Topics↗

Optical Sensors for Biomolecules Using Nanoporous Sol-Gel Materials

An important consideration for space missions to Mars is the ability to detect biosignatures. Solid-state sensing elements for optical detection of biological entities are possible using sol-gel based biologically active materials. We have used these materials as optical sensing elements in a variety of bioassays, including immunoassays and enzyme assays. By immobilizing an appropriate biomolecule in the sol-gel sensing element, we have successfully detected analytes such as amino acids and hormones. In the case of the amino acid glutamate, the enzyme glutamate dehydrogenase was the immobilized molecule, whereas in the case of the hormone cortisol, an anti-cortisol antibody was immobilized in the sensing element. In this previous work with immobilized enzymes and antibodies, excellent sensitivity and specificity were demonstrated in a variety of formats including bulk materials, thin films and fibers. We believe that the sol-gel approach is an attractive platform for bioastronautics sensing applications because of the ability to detect a wide range of entities such as amino acids, fatty acids, hopanes, porphyrins, etc. The sol-gel approach produces an optically transparent 3D silica matrix that forms around the biomolecule of interest, thus stabilizing its structure and functionality while allowing for optical detection. This encapsulation process protects the biomolecule and leads to a more "rugged" sensor. The nanoporous structure of the sol-gel matrix allows diffusion of small target molecules but keeps larger, biomolecules immobilized in the pores. We are currently developing these biologically active sol-gel materials into small portable devices for on-orbit cortisol detection

Fang, Jonathan↗

Revalidation of the Volatile Organic Analyzer Following a Major On-Orbit Maintenance Activity

The Volatile Organic Analyzer (VOA) contributes to the assessment of air quality aboard the International Space Station (ISS) by identifying and quantifying target airborne volatile organic contaminants in the module air. This on-orbit contaminant monitoring capability becomes particularly important during an air quality degradation event such as a system leak. During several ISS air quality degradations, the VOA has generated near real-time data that was used to make decisions or to better understand the contingency. The VOA was operational from January 2002 through June 2003, during which time it was validated by comparing VOA data to simultaneously acquired grab sample containers (GSCs). In January 2003, one of the two analytical channels of the VOA was shutdown because of a component failure, but a redundant channel continued to supply the necessary analytical data. In June 2003, the sole remaining channel was deactivated. Initial assessments of the channel shutdowns pointed to failed fuses or heaters, but neither was considered repairable on orbit. In 2005, it was determined that failed fuses could be replaced on orbit and the crew conducted a diagnostic procedure to identify the failed component. The crew discovered that both channels incurred failed fuses, which lead to a subsequent on orbit maintenance activity and return of the VOA to operational status in December 2005. The VOA has been providing data on the ISS atmosphere since its reactivation in 2005 and this paper will present the VOA data collected during 2006. Special emphasis will be placed upon the revalidation of the repaired VOA using GSCs as well as a summary of the diagnostic and repair procedures.

Limero, Thomas↗

Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets

Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.

Immunology↗

Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales

Enterobacterales, a large order of Gram-negative bacteria, including Escherichia coli and Klebsiella pneumoniae, are major causes of urinary tract and gastrointestinal infections, pneumonia, and other diseases in healthcare settings and communities. ESBL-producing Enterobacterales and carbapenem-resistant Enterobacterales can break down commonly used antibiotics, with some strains being resistant to all available antibiotics. This public health threat necessitates the development of novel antibiotics, ideally targeting new pathways in these bacteria. Gram-negative bacteria possess an outer membrane enriched with lipid A, a saccharolipid that serves as the membrane anchor of lipopolysaccharides and the active component of the bacterial endotoxin, causing septic shock. The biosynthesis of lipid A is crucial for the viability of Gram-negative bacteria, and as an essential enzyme in this process, LpxH has emerged as a promising target for developing novel antibiotics against multidrugresistant Gram-negative pathogens. Here, we report the development of pyridinyl sulfonyl piperazine LpxH inhibitors. Among them, ortho-substituted pyridinyl compounds significantly boost LpxH inhibition and antibiotic activity over the original phenyl series. Structural and QM/MM analyses reveal that these improved activities are primarily due to the enhanced interaction between F141 of the LpxH insertion lid and the pyridinyl group. Incorporation of the N-methyl-N-phenyl-methanesulfonamide moiety into the pyridinyl sulfonyl piperazine backbone results in JHLPH- 106 and JH-LPH-107, both of which exhibit potent antibiotic activity against wild-type Enterobacterales such as K. pneumoniae and E. coli. JH-LPH-107 exhibits a low rate of spontaneous resistance and a high safety window in vitro, rendering it an excellent lead for further clinical development.

60 APPLIED LIFE SCIENCES↗

A Voltage Inference Framework for Real-Time Observability in Active Distribution Grids

Active distribution grids are gaining traction to meet the growing environmental, socio-economic, and sustainability targets. Various advanced smart grid technologies facilitate the integration of Distributed Energy Resources (DERs) by supporting the bi-directional power flow. The limited observability of distribution grids, primarily related to their location at the very edge of power system infrastructure, brings challenges to optimal grid management. Moreover, only a limited number of measurements at regular intervals are usually available. This paper presents a novel inference framework, referred to as “Voltage Inference”, to overcome the observability issues. The proposed framework employs a prediction step based on the Multivariate Taylor series approximation, followed by a corrector step that minimizes the estimation error to infer the otherwise unknown voltages from the available measurements. Furthermore, numerical results on the IEEE 13-bus test feeder validate the accuracy and computational performance of the proposed framework.

24 POWER TRANSMISSION AND DISTRIBUTION↗