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At least 181 records · Page 10

Machine learning in nuclear materials research

Nuclear materials are often demanded to function for extended time in extreme environments, including high radiation fluxes with associated transmutations, high temperature and temperature gradients, mechanical stresses, and corrosive coolants. They also have a wide range of microstructural and chemical makeups, resulting in multifaceted and often out-of-equilibrium interactions. Machine learning (ML) is increasingly being used to tackle these complex time-dependent interactions and aid researchers in developing models and making predictions, sometimes with better accuracy than traditional modeling that focuses on one or two parameters at a time. Conventional practices of acquiring new experimental data in nuclear materials research are often slow and expensive, limiting the opportunity for data-centric ML, but new methods are changing that paradigm. Here we review high-throughput computational and experimental data approaches, especially robotic experimentation and active learning that is based on Gaussian process and Bayesian optimization. We show ML examples in structural materials (e.g., reactor pressure vessel (RPV) alloys and radiation detecting scintillating materials) and highlight new techniques of high-throughput sample preparation and characterizations, and automated radiation/environmental exposures and real-time online diagnostics. Herein, this review suggests that ML models of material constitutive relations in plasticity, damage, and even electronic and optical responses to radiation are likely to become powerful tools as they develop. Finally, we speculate on how the recent trends of using natural language processing (NLP) to aid the collection and analysis of literature data, interpretable artificial intelligence (AI), and the use of streamlined scripting, database, workflow management, and cloud computing platforms that will soon make the utilization of ML techniques as commonplace as the spreadsheet curve-fitting practices of today.

36 MATERIALS SCIENCE↗

The good, the bad, and the ugly: Data-driven load profile discord identification in a large building portfolio

Reducing the overall energy consumption and associated greenhouse gas emissions in the building sector is essential for meeting our future sustainability goals. Recently, smart energy metering facilities have been deployed to enable monitoring of energy consumption data with hourly or subhourly temporal resolution. This unprecedented data collection has created various opportunities for advanced data analytics involving load profiles (e.g., building energy benchmarking programs, building-to-grid integration, and calibration of urban-scale energy models). These applications often need preprocessing steps to detect daily load profile discords, such as: 1) outliers due to system malfunctions (the bad) and 2) irregular energy consumption patterns, such as those resulting from holidays (the ugly) compared to normal consumption patterns (the good). However, current preprocessing methods predominantly focus on filtering using statistical threshold values, which fail to capture the contextual discords of daily profiles. In addition, discord detection algorithms in building research are often aimed at finding individual building-level discords, which are not suitable at a large scale. Thus, here, we develop a method for automated load profile discord identification (ALDI) in a large portfolio of buildings (more than 100 buildings). Specifically, ALDI 1) uses the matrix profile (MP) method to quantify the similarities of daily subsequences in time series meter data, 2) compares daily MP values with typical-day MP distributions using the Kolmogorov-Smirnov test, and 3) identifies daily load profile discords in a large building portfolio. We evaluate ALDI using the metering data of both an academic campus and a residential neighborhood. Our results demonstrate that ALDI efficiently discovers measurement errors by system malfunctions and low energy consumption days in the academic campus portfolio, and it detects unique load shape patterns likely driven by occupant behavior and extreme weather conditions in the residential neighborhood.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Deep learning of experimental electrochemistry for battery cathodes across diverse compositions

Artificial intelligence (AI) has emerged as a tool for discovering and optimizing novel battery materials. However, the adoption of AI in battery cathode representation and discovery is still limited due to the complexity of optimizing multiple performance properties and the scarcity of high-fidelity data. Here, we present a machine learning model (DRXNet) for battery informatics and demonstrate the application in the discovery and optimization of disordered rocksalt (DRX) cathode materials. We have compiled the electrochemistry data of DRX cathodes over the past 5 years, resulting in a dataset of more than 19,000 discharge voltage profiles on diverse chemistries spanning 14 different metal species. Learning from this extensive dataset, our DRXNet model can capture critical features in the cycling curves of DRX cathodes under various conditions. Our approach offers a data-driven solution to facilitate the rapid identification of novel cathode materials, accelerating the development of next-generation batteries for carbon neutralization.

25 ENERGY STORAGE↗

Analysis of backwash settings to maximize net water production in an engineering-scale ultrafiltration system for water reuse

Ultrafiltration (UF) has been widely utilized as water pretreatment for different applications especially in water reuse. The UF system operation is characterized by a filtration phase, where particles accumulate on the membrane surface resulting in an increase in the transmembrane pressure (TMP) and a cleaning phase, where foulants are removed through cleaning cycles including physical backwash and chemical-enhanced backwash (CEB). In this study, data from an engineering-scale UF system treating reclaimed wastewater were used to assess the impact of backwashing on the filtration process. TMP backwash trigger, backwash duration, and CEB frequency were purposely varied for a cycle-by-cycle investigation on the net water production, water recovery, initial operating TMP, and filtration cycle duration. As the TMP backwash trigger was varied between 62 and 145kPa, the maximum net water production (63 m 3 /d) was achieved at 103kPa and water recovery remained relatively constant at approximately 92%. Backwash durations of 45, 65, and 85s were performed where both net water production and water recovery yielded similar results (~63 m 3 /d and ~ 91%) compared with 103kPa TMP backwash trigger. The CEB frequency was also lowered from one every three backwashes (1/3) to 1/6 and 1/12 and resulted in decreased net water production and water recovery while the initial TMP increased. Interestingly, the total number of CEBs remained approximately constant regardless of their frequency. In conclusion, results suggest that CEB is an important fouling control process to maximize water production.

42 ENGINEERING↗

Identifying schools at high-risk for elevated lead in drinking water using only publicly available data

Estimating the risk of lead contamination of schools' drinking water at the State level is a complex, important, and unexplored challenge. Variable water quality among water systems and changes in water chemistry during distribution affect lead dissolution rates from pipes and fittings. In addition, the locations of lead-bearing plumbing materials are uncertain. We tested the capability of six machine learning models to predict the likelihood of lead contamination of drinking water at the schools' taps using only publicly available datasets. The predictive features used in the models correspond to those with a proven correlation to the dominant, but commonly unavailable, factors that govern lead leaching: the presence of lead-bearing plumbing materials and water quality conducive to lead corrosion. By combining water chemistry data from public reports, socioeconomic information from the US census, and spatial features using Geographic Information Systems, we trained and tested models to estimate the likelihood of lead contaminated tap water in over 8,000 schools across California and Massachusetts. Our best-performing model was a Random Forest, with a 10-fold cross validation score of 0.88 for Massachusetts and 0.78 for California using the average Area Under the Receiver Operating Characteristic Curve (ROC AUC) metric. The model was then used to assign a lead leaching risk category to half of the schools across California (the other half was used for training). There was good agreement between the modeled risk categories and the actual lead leaching outcomes for every school; however, the model overestimated the lead leaching risk in up to 17% of the schools. This model is the first of its kind to offer a tool to predict the risk of lead leaching in schools at the State level. Further use of this model can help deploy limited resources more effectively to prevent childhood lead exposure from school drinking water.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Revealing latent pole and zone line information in atom probe detector maps using crystallographically correlated metrics

Poles and zone lines observed within atom probe field evaporation images are useful for a range of atom probe crystallography studies, including calibration of the reconstruction and crystallographic characterisation of microstructural features such as grain boundaries. However, this information is not always readily apparent. Techniques for plotting crystallographically correlated metrics contained within atom probe data to enhance pole and zone line contrast across the detector space are developed. This includes consideration of the electric field, molecular ions, lattice structure retained within the reconstruction, specific elemental species, the number of pulses between detection events, and the lateral distance between sequential detection events. These approaches are then applied to experimental atom probe tomography datasets on technically pure Al, nanocrystalline Al, highly doped Si, and additively manufactured Inconel 738, Haynes 282, and Ti–6Al–4V. The results facilitate the extension of atom probe crystallography studies to a broader range of crystalline datasets where crystallographic information is not readily apparent from existing methods, as well as a deeper understanding of field evaporation behaviour during an atom probe experiment.

47 OTHER INSTRUMENTATION↗

Unlocking Solutions: Innovative Approaches to Identifying and Mitigating the Environmental Impacts of Undocumented Orphan Wells in the United States

In the United States, hundreds of thousands of undocumented orphan wells have been abandoned, leaving the burden of managing environmental hazards to governmental agencies or the public. These wells, a result of over a century of fossil fuel extraction without adequate regulation, lack basic information like location and depth, emit greenhouse gases, and leak toxic substances into groundwater. For most of these wells, basic information such as well location and depth is unknown or unverified. Addressing this issue necessitates innovative and interdisciplinary approaches for locating, characterizing, and mitigating their environmental impacts. Our survey of the United States revealed the need for tools to identify well locations and assess conditions, prompting the development of technologies including machine learning to automatically extract information from old records (95%+ accuracy), remote sensing technologies like aero-magnetometers to find buried wells, and cost-effective methods for estimating methane emissions. Notably, fixed-wing drones equipped with magnetometers have emerged as cost-effective and efficient for discovering unknown wells, offering advantages over helicopters and quadcopters. Efforts also involved leveraging local knowledge through outreach to state and tribal governments as well as citizen science initiatives. These initiatives aim to significantly contribute to environmental sustainability by reducing greenhouse gases and improving air and water quality.

54 ENVIRONMENTAL SCIENCES↗

Deep Learning Enabled Strain Mapping of Single-Atom Defects in Two-Dimensional Transition Metal Dichalcogenides with Sub-Picometer Precision

Two-dimensional (2D) materials offer an ideal platform to study the strain fields induced by individual atomic defects, yet challenges associated with radiation damage have so far limited electron microscopy methods to probe these atomic-scale strain fields. In this work, we demonstrate an approach to probe single-atom defects with sub-picometer precision in a monolayer 2D transition metal dichalcogenide, WSe 2–2x Te 2x . We utilize deep learning to mine large data sets of aberration-corrected scanning transmission electron microscopy images to locate and classify point defects. By combining hundreds of images of nominally identical defects, we generate high signal-to-noise class averages which allow us to measure 2D atomic spacings with up to 0.2 pm precision. Our methods reveal that Se vacancies introduce complex, oscillating strain fields in the WSe 2–2x Te 2x lattice that correspond to alternating rings of lattice expansion and contraction. These results indicate the potential impact of computer vision for the development of high-precision electron microscopy methods for beam-sensitive materials.

2D materials↗

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity

Abstract CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

59 BASIC BIOLOGICAL SCIENCES↗

Design principles for NASICON super-ionic conductors

Na Super Ionic Conductor (NASICON) materials are an important class of solid-state electrolytes owing to their high ionic conductivity and superior chemical and electrochemical stability. In this paper, we combine first-principles calculations, experimental synthesis and testing, and natural language-driven text-mined historical data on NASICON ionic conductivity to achieve clear insights into how chemical composition influences the Na-ion conductivity. These insights, together with a high-throughput first-principles analysis of the compositional space over which NASICONs are expected to be stable, lead to the successful synthesis and electrochemical investigation of several new NASICONs solid-state conductors. Among these, a high ionic conductivity of 1.2 mS cm ₋1 could be achieved at 25 °C. We find that the ionic conductivity increases with average metal size up to a certain value and that the substitution of PO 4 polyanions by SiO 4 also enhances the ionic conductivity. While optimal ionic conductivity is found near a Na content of 3 per formula unit, the exact optimum depends on other compositional variables. Surprisingly, the Na content enhances the ionic conductivity mostly through its effect on the activation barrier, rather than through the carrier concentration. These deconvoluted design criteria may provide guidelines for the design of optimized NASICON conductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

59 BASIC BIOLOGICAL SCIENCES↗

Protein remote homology detection and structural alignment using deep learning

Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.

59 BASIC BIOLOGICAL SCIENCES↗

Fast mass spectrometry search and clustering of untargeted metabolomics data

The throughput of mass spectrometers and the amount of publicly available metabolomics data are growing rapidly, but analysis tools such as molecular networking and Mass Spectrometry Search Tool do not scale to searching and clustering billions of mass spectral data in metabolomics repositories. To address this limitation, we designed MASST+ and Networking+, which can process datasets that are up to three orders of magnitude larger than those processed by state-of-the-art tools.

59 BASIC BIOLOGICAL SCIENCES↗

Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.

59 BASIC BIOLOGICAL SCIENCES↗

Repository scale classification and decomposition of tandem mass spectral data

Various studies have shown associations between molecular features and phenotypes of biological samples. These studies, however, focus on a single phenotype per study and are not applicable to repository scale metabolomics data. Here we report MetSummarizer, a method for predicting (i) the biological phenotypes of environmental and host-oriented samples, and (ii) the raw ingredient composition of complex mixtures. We show that the aggregation of various metabolomic datasets can improve the accuracy of predictions. Since these datasets have been collected using different standards at various laboratories, in order to get unbiased results it is crucial to detect and discard standard-specific features during the classification step. We further report high accuracy in prediction of the raw ingredient composition of complex foods from the Global Foodomics Project.

59 BASIC BIOLOGICAL SCIENCES↗

Identifying COVID-19 cases and extracting patient reported symptoms from Reddit using natural language processing

We used social media data from “covid19positive” subreddit, from 03/2020 to 03/2022 to identify COVID-19 cases and extract their reported symptoms automatically using natural language processing (NLP). We trained a Bidirectional Encoder Representations from Transformers classification model with chunking to identify COVID-19 cases; also, we developed a novel QuadArm model, which incorporates Question-answering, dual-corpus expansion, Adaptive rotation clustering, and mapping, to extract symptoms. Our classification model achieved a 91.2% accuracy for the early period (03/2020-05/2020) and was applied to the Delta (07/2021–09/2021) and Omicron (12/2021–03/2022) periods for case identification. We identified 310, 8794, and 12,094 COVID-positive authors in the three periods, respectively. The top five common symptoms extracted in the early period were coughing (57%), fever (55%), loss of sense of smell (41%), headache (40%), and sore throat (40%). During the Delta period, these symptoms remained as the top five symptoms with percent authors reporting symptoms reduced to half or fewer than the early period. During the Omicron period, loss of sense of smell was reported less while sore throat was reported more. Our study demonstrated that NLP can be used to identify COVID-19 cases accurately and extracted symptoms efficiently.

60 APPLIED LIFE SCIENCES↗

Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures

Abstract The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.

59 BASIC BIOLOGICAL SCIENCES↗