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At least 1,405 records · Page 78

Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster

Protein expression levels are regulated through both translation and degradation mechanisms. Levels of degradation intermediates, i.e., partially degraded proteins, cannot be distinguished from those of intact proteins by global proteomics analysis, which quantify total protein abundance levels. This study aimed to develop a tool for assessing the aspects of degradation regulation via proteolytic processing through a new multiplexed N-terminomics method involving selective isobaric labeling of protein N-termini and immunoaffinity capture of the labeled N-terminal peptides. Our method allows for not only identification or proteolytic cleavage sites, but also highly multiplexed quantification of proteolytic processing. In this paper, we profiled a number of potential cleavage sites by signal peptidase and provided experimental confirmation of predicted cleavage sites of signal peptide. Furthermore, the present method uniquely represents the landscape of proteomic proteolytic processing rate during early embryogenesis in Drosophila melanogaster, revealing the underlying mechanism of stringent decay regulation of zygotically expressed proteins during early stages of embryogenesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncovering the predictive pathways of lithium and sodium interchange in layered oxides

Ion exchange is a powerful method to access metastable materials with advanced functionalities for energy storage applications. However, high concentrations and unfavourably large excesses of lithium are always used for synthesizing lithium cathodes from parent sodium material, and the reaction pathways remain elusive. Here, using layered oxides as model materials, we demonstrate that vacancy level and its corresponding lithium preference are critical in determining the accessible and inaccessible ion exchange pathways. Taking advantage of the strong lithium preference at the right vacancy level, we establish predictive compositional and structural evolution at extremely dilute and low excess lithium based on the phase equilibrium between Li 0.94 CoO 2 and Na 0.48 CoO 2 . Such phase separation behaviour is general in both surface reaction-limited and diffusion-limited exchange conditions and is accomplished with the charge redistribution on transition metals. Guided by this understanding, we demonstrate the synthesis of Na y CoO 2 from the parent Li x CoO 2 and the synthesis of Li 0.94 CoO 2 from Na y CoO 2 at 1-1,000 Li/Na (molar ratio) with an electrochemical assisted ion exchange method by mitigating the kinetic barriers. Our study opens new opportunities for ion exchange in predictive synthesis and separation applications. Ion exchange is a powerful method to access metastable materials for energy storage, but identifying lithium and sodium interchange in layered oxides remains challenging. Using such model materials, vacancy level and corresponding lithium preference are shown to be crucial for ion exchange pathway accessibility.

25 ENERGY STORAGE↗

Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics

Computational methods for creating in silico libraries of molecular descriptors (e.g., collision cross sections) are becoming increasingly prevalent due to the limited number of authentic reference materials available for traditional library building. These so-called “reference-free metabolomics” methods require sampling sets of molecular conformers in order to produce high accuracy property predictions. Due to the computational cost of the subsequent calculations for each conformer, there is a need to sample the most relevant subset and avoid repeating calculations on conformers that are nearly identical. The goal of this study is to introduce a heuristic method of finding the most dissimilar conformers from a larger population in order to help speed up reference-free calculation methods and maintain a high property prediction accuracy. Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population size grows large. Because there exists a pairwise relationship between each item and all other items in the population, finding the set of the n most dissimilar items is different than simply sorting an array of numbers. For instance, if you have a set of the most dissimilar n = 4 items, one or more of the items from n = 4 might not be in the set n = 5. An exact solution would have to search all possible combinations of size n in the population exhaustively. We present an open-source software called similarity downselection (SDS), written in Python and freely available on GitHub. SDS implements a heuristic algorithm for quickly finding the approximate set(s) of the n most dissimilar items. We benchmark SDS against a Monte Carlo method, which attempts to find the exact solution through repeated random sampling. We show that for SDS to find the set of n most dissimilar conformers, our method is not only orders of magnitude faster, but it is also more accurate than running Monte Carlo for 1,000,000 iterations, each searching for set sizes n = 3–7 out of a population of 50,000. We also benchmark SDS against the exact solution for example small populations, showing that SDS produces a solution close to the exact solution in these instances. Using theoretical approaches, we also demonstrate the constraints of the greedy algorithm and its efficacy as a ratio to the exact solution.

97 MATHEMATICS AND COMPUTING↗

Trust in Artificial Intelligence: Meta-Analytic Findings

Objective The present meta-analysis sought to determine significant factors that predict trust in artificial intelligence (AI). Such factors were divided into those relating to (a) the human trustor, (b) the AI trustee, and (c) the shared context of their interaction. Background There are many factors influencing trust in robots, automation, and technology in general, and there have been several meta-analytic attempts to understand the antecedents of trust in these areas. However, no targeted meta-analysis has been performed examining the antecedents of trust in AI. Method Data from 65 articles examined the three predicted categories, as well as the subcategories of human characteristics and abilities, AI performance and attributes, and contextual tasking. Lastly, four common uses for AI (i.e., chatbots, robots, automated vehicles, and nonembodied, plain algorithms) were examined as further potential moderating factors. Results Results showed that all of the examined categories were significant predictors of trust in AI as well as many individual antecedents such as AI reliability and anthropomorphism, among many others. Conclusion Overall, the results of this meta-analysis determined several factors that influence trust, including some that have no bearing on AI performance. Additionally, we highlight the areas where there is currently no empirical research. Application Findings from this analysis will allow designers to build systems that elicit higher or lower levels of trust, as they require.

Behavioral Sciences↗

The Optical and Infrared Are Connected

Galaxies are often modeled as composites of separable components with distinct spectral signatures, implying that different wavelength ranges are only weakly correlated. They are not. We present a data-driven model that exploits subtle correlations between physical processes to accurately predict infrared (IR) Wide-field Infrared Survey Explorer (WISE) photometry from a neural summary of optical Sloan Digital Sky Survey spectra. The model achieves accuracies of $χ^{2}_{N} ≈ 1$ for all photometric bands in WISE, as well as good colors. We are able to tightly constrain typically IR-derived properties, e.g., the bolometric luminosities of active galactic nuclei (AGN) and dust parameters such as q PAH . We also test whether current spectral energy distribution (SED) fitting methods reproduce such panchromatic relations, but find their predictions biased and overconfident, likely due to model misspecification, with correlated biases in star-formation rates (SFRs) and AGN luminosities being most evident. To help improve SED models, we determine which features of the optical spectrum are responsible for our improved predictions, and identify several lines (Ca II , Sr II , Fe I , [O II ], and Hα), which point to the complex chronology of star formation and chemical enrichment being incorrectly modeled.

Jespersen, Christian Kragh [Princeton Univ., NJ (U↗

Machine Learning Predicts the Timing and Shear Stress Evolution of Lab Earthquakes Using Active Seismic Monitoring of Fault Zone Processes

Abstract Machine learning (ML) techniques have become increasingly important in seismology and earthquake science. Lab‐based studies have used acoustic emission data to predict time‐to‐failure and stress state, and in a few cases, the same approach has been used for field data. However, the underlying physical mechanisms that allow lab earthquake prediction and seismic forecasting remain poorly resolved. Here, we address this knowledge gap by coupling active‐source seismic data, which probe asperity‐scale processes, with ML methods. We show that elastic waves passing through the lab fault zone contain information that can predict the full spectrum of labquakes from slow slip instabilities to highly aperiodic events. The ML methods utilize systematic changes in P‐wave amplitude and velocity to accurately predict the timing and shear stress during labquakes. The ML predictions improve in accuracy closer to fault failure, demonstrating that the predictive power of the ultrasonic signals improves as the fault approaches failure. Our results demonstrate that the relationship between the ultrasonic parameters and fault slip rate, and in turn, the systematically evolving real area of contact and asperity stiffness allow the gradient boosting algorithm to “learn” about the state of the fault and its proximity to failure. Broadly, our results demonstrate the utility of physics‐informed ML in forecasting the imminence of fault slip at the laboratory scale, which may have important implications for earthquake mechanics in nature.

58 GEOSCIENCES↗

Carbon fiber classification using raman spectroscopy

Carbon fiber characterization processes are described that include multi-condition Raman spectroscopy-based examination combined with multivariate data analyses. Methods are a nondestructive material characterization approach that can provide predictions as to carbon fiber bulk physical properties, as well as identification of unknown carbon fiber materials for quality control purposes. The framework of the multivariate analysis methods includes a principal component-based identification protocol including comparison of Raman spectral data from an unknown carbon fiber with a data library of multiple principal component spaces.

Houk, Amanda L.↗

Tuning Multigrid Methods with Robust Optimization and Local Fourier Analysis

Local Fourier analysis is a useful tool for predicting and analyzing the performance of many efficient algorithms for the solution of discretized PDEs, such as multigrid and domain decomposition methods. The crucial aspect of local Fourier analysis is that it can be used to minimize an estimate of the spectral radius of a stationary iteration, or the condition number of a preconditioned system, in terms of a symbol representation of the algorithm. In practice, this is a “minimax” problem, minimizing with respect to solver parameters the appropriate measure of work, which involves maximizing over the Fourier frequency. Often, several algorithmic parameters may be determined by local Fourier analysis in order to obtain efficient algorithms. Analytical solutions to minimax problems are rarely possible beyond simple problems; the status quo in local Fourier analysis involves grid sampling, which is prohibitively expensive in high dimensions. In this paper, we propose and explore optimization algorithms to solve these problems efficiently. Finally, several examples, with known and unknown analytical solutions, are presented to show the effectiveness of these approaches.

97 MATHEMATICS AND COMPUTING↗

Image-driven discriminative and generative machine learning algorithms for establishing microstructure–processing relationships

We investigate methods of microstructure representation for the purpose of predicting processing condition from microstructure image data. A binary alloy that is currently under development as a nuclear fuel was studied for the purpose of developing an improved machine learning approach to image recognition, characterization, and building predictive capabilities linking microstructure to processing conditions. Here, we test different microstructure representations and evaluate model performance based on classification accuracy. A classification accuracy of 95.8% was achieved fordistinguishing between micrographs corresponding to ten different thermo-mechanical material processing conditions.We find that our newly developed microstructure representation describes image data well, and the traditional approachof utilizing area fractions of different phases is insufficient for distinguishing between multiple classes using a relativelysmall, imbalanced original data set of 272 images. To explore the applicability of generative methods for supplementing such limited data sets, generative adversarial networks were trained to generate artificial microstructure images. Two different generative networks were trained and tested to assess performance. Challenges and best practices associated with applying machine learning to limited microstructure image data sets is also discussed. Our work has implications for quantitative microstructure analysis, and development of microstructure-processing relationships in limited data sets typical of metallurgical process design studies.

36 MATERIALS SCIENCE↗

Pit Stability Predictions of Additively Manufactured SS316 Surfaces Using Finite Element Analysis

Stainless steels are susceptible to localized forms of corrosion attack, such as pitting. The size and lifetime of a nucleated pit can vary, depending on a critical potential or current density criterion, which determines if the pit repassivates or continues growing. This work uses finite element method (FEM) modeling to compare the critical pit radii predicted by thermodynamic and kinetic repassivation criteria. Experimental electrochemical boundary conditions are used to capture the active pit kinetics. Geometric and environmental parameters, such as the pit shape and size (analogous to additively manufactured lack-of-fusion pores), solution concentration, and water layer thickness were considered to assess their impact on the pit repassivation criterion. The critical pit radius (the transition point from stable growth to repassivation) predicted for a hemispherical pit was larger when using the repassivation potential (E rp ) criteria, as opposed to the current density criteria (pit stability product). Including both the pit stability product and E rp into its calculations, the analytical maximum pit model predicted a critical radius two times more conservative than the FEA approach, under the conditions studied herein. The complex pits representing lack-of-fusion pores were shown to have minimal impact on the critical radius in atmospheric conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of Partial Least Squares Approaches to Pyroprocessing ER Data

Multivariate approaches show promise for application to process monitoring for safeguards of pyroprocessing. Past MPACT work explored the application of Principal Component Analysis (PCA) to detect off-normal conditions in pyroprocessing electrorefiner (ER) data from in the Hot Fuel Examination Facility (HFEF) at Idaho National Laboratory (INL) known as the Scalable Pyrochemical Recycling testbed (SPyRe) ER. PCA, however, does not consider the output variables. In FY24, multivariate analysis was extended from PCA to Partial Least Squares (PLS) analysis. PLS maximizes the variance between both the input signals and output variables. In the case of this work, PLS was applied in two different manners: Predictive PLS and Discriminant PLS. Predictive PLS maximizes the covariance between the process variables of the ER and the measured U concentration from in-situ voltammetry. Discriminant PLS maximizes the covariance between the process variables and a set of training process “states” such as known off-normal conditions. By projecting into the latent variable space in PLS, the process variables can be regressed onto the outputs and predictions can be made for new data sets. In this work, by applying predictive PLS, a penalized non-linear PLS approach was able to make predictions of concentration based on test and training data and detect when operations were off-normal. However, the predictive PLS does not classify the signals to which off-normal operations are attributable. Discriminant PLS can be used to classify off-normal operations but is inadequate to properly classify specific off-normal classes like power supply faults when the Discriminant PLS model is only specifically trained to detect that off-normal class. When all faults are trained against the observation data, all three operational classes are accurately classified and distinguished. Thus, future application of latent variable techniques should not select any given method, but should use a mixture of PCA, Predictive PLS, and Discriminant PLS.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Physics-Guided Machine Learning for Prediction of Cloud Properties in Satellite-Derived Solar Data

With over 20 years of high-resolution surface irradiance data covering most of the western hemisphere, the National Solar Radiation Database (NSRDB) is a vital public data asset. The NSRDB uses a two-step Physical Solar Model (PSM) that explicitly considers the effects of clouds and other atmospheric variables on radiative transfer. High-quality physical and optical cloud properties derived from satellite imagery are perhaps the most important data inputs to the PSM, representing the greatest source of radiation attenuation and scattering. However, traditional methods for cloud property retrieval have their own limitations and are unable to accurately predict cloud properties outside of nominal conditions. We introduce a physics-guided neural network that can accurately predict cloud properties when traditional methods fail or are inaccurate. Using this framework, we show reductions in relative Root Mean Square Error (RMSE) for Global Horizontal Irradiance (GHI) up to 13 percentage points for timesteps that previously had missing or low-quality cloud property data. We expect that this methodology will be effective in improving the quality of cloud property and solar irradiance data in the NSRDB.

cloud properties↗

Machine learning nonequilibrium electron forces for spin dynamics of itinerant magnets

Abstract We present a generalized potential theory for conservative as well as nonconservative forces for the Landau-Lifshitz magnetization dynamics. Importantly, this formulation makes possible an elegant generalization of the Behler-Parrinello machine learning (ML) approach, which is a cornerstone of ML-based quantum molecular dynamics methods, to the modeling of force fields in adiabatic spin dynamics of out-of-equilibrium itinerant magnetic systems. We demonstrate our approach by developing a deep-learning neural network that successfully learns the electron-mediated exchange fields in a driven s-d model computed from the nonequilibrium Green’s function method. We show that dynamical simulations with forces predicted from the neural network accurately reproduce the voltage-driven domain-wall propagation. Our work also lays the foundation for ML modeling of spin transfer torques and opens a avenue for ML-based multi-scale modeling of nonequilibrium dynamical phenomena in itinerant magnets and spintronics.

36 MATERIALS SCIENCE↗

Synthesis of inter‐lanthanide sesquioxides LnLn'O 3 by polymeric steric entrapment

Lanthanide oxides are well known in the fields of optical, electronic, and magnetic materials. Even so, there are many application spaces yet to be explored. Previous modeling of inter-lanthanide sesquioxides, in which the compound contains two lanthanide cations, predicts the lowest level energy structure as a function of chemistry, which this work seeks to verify. Three materials of interest, ErLuO 3 , LaLuO 3 , and SmLuO 3 , were synthesized for the first time by the polymeric steric entrapment (PSE) method. X-ray diffraction confirms the stable state predictions of ErLuO 3 and SmLuO 3 forming a bixbyite type structure and LaLuO 3 forming a perovskite type structure. This work demonstrates PSE as a viable and reliable route toward the synthesis of these unique materials.

36 MATERIALS SCIENCE↗

Physics-Guided Machine Learning for Prediction of Cloud Properties in Satellite-Derived Solar Data: Preprint

With over 20 years of high-resolution surface irradiance data covering most of the western hemisphere, the National Solar Radiation Database (NSRDB) is a vital public data asset. The NSRDB uses a two-step Physical Solar Model (PSM) that explicitly considers the effects of clouds and other atmospheric variables on radiative transfer. High-quality physical and optical cloud properties derived from satellite imagery are perhaps the most important data input to the PSM, representing the greatest source of radiation attenuation and scattering. However, traditional methods for cloud property retrieval have their own limitations and are unable to accurately predict cloud properties outside of nominal conditions. We introduce a physics-guided neural network that can accurately predict cloud properties when traditional methods fail or are inaccurate. Using this framework, we show reductions in relative Root Mean Square Error (RMSE) for Global Horizontal Irradiance (GHI) up to 13 percentage points for timesteps that previously had missing or low-quality cloud property data. We expect that this methodology will be effective in improving the quality of cloud property and solar irradiance data in the NSRDB.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Surrogate Model Based Optimization for Finding Robust Deep Learning Model Architectures

Deep Learning (DL) models are increasingly used throughout the sciences. However, their performance and usefulness depend greatly on their architecture which is defined by hyperparameters such as the number of nodes, layers, the learning rate, etc. Tuning these hyperparameters is time-consuming because evaluating their performance requires a lengthy training step. Stochastic optimizers used in training lead to performance variability and potentially prediction reliability issues. In this talk, we will describe an automated optimization method based on surrogate models and active learning strategies for tuning DL model architectures. We take into account the prediction variability with the goal to identify architectures that make reliable and robust predictions. We demonstrate our developments on an application arising in particle physics.

deep learning↗

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗

A “Master Curve” Describing Reaction Inhomogeneity and Plating Onset during Fast-Charging of Graphite Electrodes

Lithium plating in porous graphite electrodes is a major limitation for fast charging. Theoretical evidence suggests plating during fast charging is largely due to inhomogeneous intercalation through the electrode thickness (caused by ionic/mass transfer limitations and inherent thermodynamic properties of the graphite material). Numerical and analytical predictions of plating onset during fast charging have been proposed but not compared directly with experiments. This work validates these model predictions against plating onset measurements via the “dOCV” method in graphite half-cells, for various electrode thicknesses and C-rates. Remarkably, it is shown that experimental and theoretical trends in plating onset (vs C-rate and electrode thickness) collapse to a single “master curve” using a nondimensional “reaction inhomogeneity” parameter. This observation supports the hypothesized reaction inhomogeneity mechanism for accelerating plating onset and provides practical guidance for electrode design. Furthermore, this work develops theory to quantify reaction inhomogeneity in situ directly from voltage V vs capacity Q data, using dQ / dV analysis. Here again, experiments and numerical predictions show good agreement, where peaks that correspond to LiC 6 correlate with plating onset. This work provides experimental validation of theoretical tools that can predict plating onset, aid electrode design, and give insight for plating onset mechanisms during fast charging.

25 ENERGY STORAGE↗