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At least 1,333 records · Page 74

A high-throughput workflow to analyze sequence-conformation relationships and explore hydrophobic patterning in disordered peptoids

Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using matrix-assisted laser desorption/ionization and tandem mass spectrometry (MALDI-MS/MS), and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived “motifs” to inform a machine-learning algorithm toward conformation prediction. Here, this multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.

data-driven analysis↗

Deep eutectic solvents in separations: Methods of preparation, polarity, and applications in extractions and capillary electrochromatography

Deep eutectic solvents (DESs) have emerged as alternatives to conventional organic solvents and ionic liquids (ILs). Their tunable and designer physio-chemical properties, low cost, and ease of preparation make them attractive solvent systems for use in extractions and additives to chromatographic separations. However, due to the diverse range of hydrogen bond acceptors and donors that comprise DESs, choosing the appropriate solvent for separations can be challenging. This work discusses all methods of DES preparation and details their advantages and disadvantages. Since polarity is an important aspect in their use in separations, the classification of DESs based on the betaine dye and nile red scales as well as Kamlet-Taft parameters is also discussed. Finally, a summary of applications of DESs in various extraction processes (phenolics, fuels, metals, proteins, carbohydrates), solid-phase extraction, solid-phase microextraction, as well as capillary electrochromatography is provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparison of Machine Learning and Deep Learning for View Identification from Cardiac Magnetic Resonance Images

Background: Artificial intelligence is increasingly utilized to aid in the interpretation of cardiac magnetic resonance (CMR) studies. One of the first steps is the identification of the imaging plane depicted, which can be achieved by both deep learning (DL) and classical machine learning (ML) techniques without user input. We aimed to compare the accuracy of ML and DL for CMR view classification and to identify potential pitfalls during training and testing of the algorithms. Methods: To train our DL and ML algorithms, we first established datasets by retrospectively selecting 200 CMR cases. The models were trained using two different cohorts (passively and actively curated) and applied data augmentation to enhance training. Once trained, the models were validated on an external dataset, consisting of 20 cases acquired at another center. We then compared accuracy metrics and applied class activation mapping (CAM) to visualize DL model performance. Results: The DL and ML models trained with the passively-curated CMR cohort were 99.1% and 99.3% accurate on the validation set, respectively. However, when tested on the CMR cases with complex anatomy, both models performed poorly. After training and testing our models again on all 200 cases (active cohort), validation on the external dataset resulted in 95% and 90% accuracy, respectively. The CAM analysis depicted heat maps that demonstrated the importance of carefully curating the datasets to be used for training. Conclusions: Both DL and ML models can accurately classify CMR images, but DL outperformed ML when classifying images with complex heart anatomy.

artificial intelligence↗

An adaptive and stability-promoting layerwise training approach for sparse deep neural network architecture

This work presents a two-stage adaptive framework for progressively developing deep neural network (DNN) architectures that generalize well for a given training data set. In the first stage, a layerwise training approach is adopted where a new layer is added each time and trained independently by freezing parameters in the previous layers. We impose desirable structures on the DNN by employing manifold regularization, sparsity regularization, and physics-informed terms. We introduce a ε – δ – stability-promoting concept as a desirable property for a learning algorithm and show that employing manifold regularization yields a ε – δ stability-promoting algorithm. Further, we also derive the necessary conditions for the trainability of a newly added layer and investigate the training saturation problem. In the second stage of the algorithm (post-processing), a sequence of shallow networks is employed to extract information from the residual produced in the first stage, thereby improving the prediction accuracy. Numerical investigations on prototype regression and classification problems demonstrate that the proposed approach can outperform fully connected DNNs of the same size. Moreover, by equipping the physics-informed neural network (PINN) with the proposed adaptive architecture strategy to solve partial differential equations, we numerically show that adaptive PINNs not only are superior to standard PINNs but also produce interpretable hidden layers with provable stability. As a result, we also apply our architecture design strategy to solve inverse problems governed by elliptic partial differential equations.

42 ENGINEERING↗

Data-driven selection of stiff chemistry ODE solver in operator-splitting schemes

Most computational fluid dynamics simulations of practical combustion applications employ operator-splitting schemes, where chemistry and transport are separated and integrated with distinct numerical methods. The changes in composition due to chemistry are evaluated by solving ordinary differential equations (ODE) in each cell of the computational domain, which typically dominates the computational cost when detailed chemistry is considered. In this work, a data-driven approach for the selection of chemistry ODE solvers in operator-splitting schemes is presented. Neural networks are used to predict the ODE solvers CPU times and errors for a given thermochemical state. This allows the selection of an optimal ODE solver on a cell-by-cell, timestep-by-timestep basis. The models are trained using a wide set of thermochemical states generated through partially-stirred reactors and flames simulations. The methodology is validated by quantifying the prediction errors, the classification accuracy, and the computational speedup. The model predicts the optimal ODE solver for 70 to 95% of the validation cases and decreases the computional cost by a factor of 3 or more. The generalizability of the methodology to different chemical mechanisms and different fuels is assessed and it is shown that the model’s performance is only slightly degraded and its applicability is significantly enhanced if the inputs to the neural networks are restricted to a small set of thermochemical state variables present in most chemical mechanisms. In conclusion, the models are used in an homogeneous reactor case and a multi-dimensional CFD simulation of a diesel spray at high pressure where a speedup of more than 3 is achieved.

42 ENGINEERING↗

On the hot surface ignition of a wall-stagnating spray flame

The ignition of fuel sprays due to interaction with hot surfaces is an important phenomenon in the safety analysis of many engineering systems. We perform a parametric study of the hot surface ignition (HSI) of a fuel spray approaching a heated surface caused by the accidental leakage of a fuel line. Here, to this end, we employ a one-dimensional Eulerian-Eulerian formulation with a non-equilibrium evaporation model and a realistic chemical mechanism to describe $n$-dodecane fuel chemistry. We first describe and analyze the phenomenology of the unsteady processes leading to ignition using non-dimensionalized quantities. Through consideration of the temporal development of the most reactive mixture, we demonstrate that ignition occurs at a fuel-lean composition in a premixed region near the hot surface. Using non-dimensional parameters identified from the governing equations, we perform a parametric study of the time, location and local mixture composition at ignition and determine the ignition limits. We then identify the most important parametric sensitivities for physical analysis using a data-driven classification method. Our analysis demonstrates a contraction of the ignition limits with increased Stokes number and a regime of parametric insensitivity of igniting mixture composition. We also show that at high Damköhler numbers, the ignition location conforms to the parametric behavior of the thermal boundary layer, whereas at low Damköhler numbers approaching the ignition limit it reaches a near-unity value of the quenching Peclet number. We then compare the demonstrated parametric dependencies to the results of the quasi-steady asymptotic ignition literature, showing that our results are consistent with those obtained analytically within the limitations imposed by the simplified formulation of the latter.

42 ENGINEERING↗

Machine learning for interpreting coherent X-ray speckle patterns

Speckle patterns produced by coherent X-ray have a close relationship with the internal structure of materials but quantitative inversion of the relationship to determine structure from speckle patterns is challenging. Here, in this work, we investigate the link between coherent X-ray speckle patterns and sample structures using a model 2D disk system and explore the ability of machine learning to learn aspects of the relationship. Specifically, we train a deep neural network to classify the coherent X-ray speckle patterns according to the disk number density in the corresponding structure. It is demonstrated that the classification system is accurate for both non-disperse and disperse size distributions.

36 MATERIALS SCIENCE↗

NanoPSD: A software for automatic detection of Nano-Particle Shape Distribution in electron microscopy images

Accurate quantification of the size and morphology of nanoparticles from electron microscopy (EM) images is essential to understand growth mechanisms, surface reactivity, and functional behavior in nanoscale materials. Manual analysis remains slow, subjective, and difficult to reproduce in large datasets. We introduce NanoPSD (Nano-Particle Shape Distribution), an open-source and fully automated framework for quantitative particle detection and morphology analysis from EM images. NanoPSD integrates adaptive contrast enhancement, polarity-agnostic scale-bar detection, Optical Character Recognition (OCR)-based calibration, and classical segmentation via Otsu thresholding with morphological refinement. Particle contours are used to extract geometric descriptors, including equivalent circular diameter, aspect ratio, circularity, and solidity, enabling automated classification into spherical, rod-like, and aggregate morphologies. The framework supports both single-image and batch processing, generating publication-quality visualizations, LaTeX-ready tables, and structured comma-separated values (CSV) datasets. As a demonstration, we applied NanoPSD to plasma-synthesized nanoparticle samples diagnosed via transmission electron microscopy (TEM). The code produced statistically robust size and morphology distributions spanning a few to tens of nanometers with minimal user supervision. The pipeline demonstrates high reproducibility and scalability, processing large image collections with consistent calibration and output formatting. Its modular design enables seamless integration of future deep-learning-based segmentation models, providing a pathway toward intelligent, data-driven electron microscopy analysis.

36 MATERIALS SCIENCE↗

Microstructure prediction for Ti-22Al-25Nb in laser powder bed fusion

This work presents a physics-informed framework for predicting solidification morphology and defect susceptibility in additively manufactured Ti–22Al–25Nb across a broad processing space. The framework integrates solidification microstructure selection (SMS) analysis with a single-track defect-based printability map to establish a unified methodology linking processing parameters to both interfacial morphology and manufacturability. Thermal gradients G and solidification rates R are first computed using the Thermo-Calc Additive Manufacturing (TC-AM) module, a finite-interface-dissipation (FID) phase-field (PF) model coupled with CALPHAD method is then employed to systematically distinguish planar and dendritic regimes as functions of $G$ and $R$. By superimposing the printability map onto the morphology projections, a comprehensive process–structure framework is obtained. Across most processing conditions, the predicted microstructure is predominantly dendritic, while planar growth emerges only under selected laser power $P$ and scan speed $v$ combinations. In addition to morphology classification, the framework quantifies the dendritic area fraction and introduces a width-based morphology descriptor to characterize the spatial extent of planar/dendritic regions within the melt pool. It provides mechanistic insight into the interplay between solidification physics and defect formation, offering practical guidance for parameter selection and microstructural control in Ti–22Al–25Nb additive manufacturing (AM).

36 MATERIALS SCIENCE↗

PlasmoData.jl — A Julia framework for modeling and analyzing complex data as graphs

Datasets encountered in scientific and engineering applications appear in complex formats (e.g., images, multivariate time series, molecules, video, text strings, networks). Graph theory provides a unifying framework to model such datasets and enables the use of powerful tools that can help analyze, visualize, and extract value from data. In this work, we present PlasmoData.jl, an open-source, Julia framework that uses concepts of graph theory to facilitate the modeling and analysis of complex datasets. The core of our framework is a general data modeling abstraction, which we call a DataGraph. We show how the abstraction and software implementation can be used to represent diverse data objects as graphs and to enable the use of tools from topology, graph theory, and machine learning (e.g., graph neural networks) to conduct a variety of tasks. We illustrate the versatility of the framework by using real datasets: (i) an image classification problem using topological data analysis to extract features from the graph model to train machine learning models; (ii) a disease outbreak problem where we model multivariate time series as graphs to detect abnormal events; and (iii) a technology pathway analysis problem where we highlight how we can use graphs to navigate connectivity. Further, our discussion also highlights how PlasmoData.jl leverages native Julia capabilities to enable compact syntax, scalable computations, and interfaces with diverse packages. Overall, we show that the DataGraph abstraction and PlasmoData.jl Julia package are able to model data within graphs and enable useful analysis.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

IrRep: Symmetry eigenvalues and irreducible representations of ab initio band structures

Here, we present IrRep – a Python code that calculates the symmetry eigenvalues of electronic Bloch states in crystalline solids and the irreducible representations under which they transform. As input it receives bandstructures computed with state-of-the-art Density Functional Theory codes such as VASP, Quantum Espresso, or Abinit, as well as any other code that has an interface to Wannier90. Our code is applicable to materials in any of the 230 space groups and double groups preserving time-reversal symmetry with or without spin-orbit coupling included, for primitive or conventional unit cells. This makes IrRep a powerful tool to systematically analyze the connectivity and topological classification of bands, as well as to detect insulators with non-trivial topology, following the Topological Quantum Chemistry formalism: IrRep can generate the input files needed to calculate the (physical) elementary band representations and the symmetry-based indicators using the [CheckTopologicalMat: https://www.cryst.ehu.es/cgi-bin/cryst/programs/magnetictopo.pl] routine of the Bilbao Crystallographic Server. It is also particularly suitable for interfaces with other plane-waves based codes, due to its flexible structure.

97 MATHEMATICS AND COMPUTING↗

Maximizing dynamic range and performance of anatase TiO 2 ECRAM through structure and programming

Here, in this study, we investigate the structure-dependent modulation characteristics of all-solid-state three-terminal electrochemical random-access memory (ECRAM) based on an anatase Li x TiO 2 channel. By directly comparing “asymmetric” and “symmetric” ECRAM device architectures, we reveal significant insight into the impact of a non-zero gate-drain open-circuit voltage and its influence on voltage vs. current-controlled gating. We also explore the impact of potentiation/depression write parameters on the symmetry, linearity, and dynamic range of the device response. Together, initial results from optimizing structure and programming approaches yielded unprecedented G max /G min ratios of >1,000 for ECRAM and hundreds of tunable memory states with excellent linearity and symmetry. Simulations based on these ECRAM devices further illustrate the promise of this analog memory technology, achieving near 2% classification error in the MNIST digit recognition benchmark for a range of training parameters compared to a theoretical best of 1.66% and outperforming other device models extracted from the literature.

AIHWKit↗

Leveraging large language models to address data scarcity in machine learning for graphene synthesis

Machine learning in experimental materials science faces significant challenges due to the scarcity of data, which are costly and time-consuming to generate, particularly when relying on in-house experiments. Literature data mining offers a potential solution but introduces issues like mixed data quality, inconsistent formats, and non-uniform reporting of synthesis parameters, resulting in partially missing and heterogeneous features across the dataset. Here, we propose data imputation and feature engineering methods that employ pre-trained large language models (LLMs) to enhance machine learning performance on scarce, heterogeneous datasets, demonstrated on graphene CVD synthesis data and the ML-HydPARK hydrogen storage dataset. GPT models perform data imputation via tailored prompting and semantic normalization of inconsistently reported features through embeddings, for example, to harmonize the complex nomenclature of CVD substrates. Beyond yielding more diverse and richer feature representations than traditional methods such as K-nearest neighbors (KNN) and Multivariate Imputation by Chained Equations (MICE), LLM-based data imputation is evaluated against dataset characteristics and prompting strategies. We vary the level of autonomy granted to the LLM, from generic prompting that leverages pre-trained knowledge for autonomous data generation to data-informed prompting that constrains outputs using target-specific information, and demonstrate which level of autonomy yields superior imputation performance across datasets and feature types. The proposed data engineering methods markedly improve downstream performance; for example, in graphene layer number classification using a support vector machine (SVM), binary accuracy increases from 39% to 65% and ternary accuracy from 52% to 72%. Fine-tuning experiments on both datasets show that combining our proposed LLM-based data imputation and feature encoding methods with numerical machine learning predictors outperforms standalone fine-tuned LLM predictors in data-scarce settings. The proposed strategies emphasize data enhancement techniques rather than refining learning architectures or regularizing loss functions, offering a broadly applicable framework for improving machine learning performance on scarce, inhomogeneous datasets.

Chemical vapor deposition↗

Characterizing Long COVID: Deep Phenotype of a Complex Condition

Background: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. Methods: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. Funding: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. Interpretation: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID.

60 APPLIED LIFE SCIENCES↗

Defining an industrial heat pump: A review & synthesis

Clear and understandable definitions of advanced energy technologies are not common and often confuse those who are not experts. This review paper addresses a critical issue in the field of heat pumps: the ambiguity surrounding the term “industrial heat pump.” The term, as discussed in various literature and media, often leads to misconceptions about the capabilities and applications of heat pumps, particularly in industrial contexts. This review paper seeks to refine and unify the definition of industrial heat pumps by analyzing existing academic and commercial literature, industry reports, and classifications. Unique identifiers explored for the definition of an industrial heat pump include the use of waste heat, operating temperature ranges, size specifications, and specific end-use applications. The study reveals differences in how industrial heat pumps are defined in academic and commercial contexts, highlighting the need for a standardized definition to facilitate better communication among manufacturers, policymakers, and end users. This is especially important considering recent legislative efforts such as the HEAT Act, which seeks to promote industrial heat pump adoption. The proposed definition aims to provide clarity while supporting the effective deployment of industrial heat pumps. With proper adoption, the definition will help promote the role of industrial heat pumps in achieving energy efficiency goals in the industrial sector. The intended impact is for the definition to serve as a foundational reference for future research and policy development.

Heat pump characteristics↗

A spatiotemporally explicit and scalable indicator of intact lands across the conterminous United States, 1986–2023

Globally, ecologically intact areas are increasingly scarce. Agricultural expansion into previously uncultivated areas drives the loss of intact lands that might otherwise exhibit high levels of ecological integrity. Thus, the absence of cultivation can be an indicator of intact lands as measured from remote sensing data and thematic maps. Our objective for this study was to develop and compare tractable approaches based on remotely sensed satellite data to map spatial patterns of potentially intact lands across the conterminous U.S. (CONUS). Using annual cultivation probabilities derived from satellite observations, we classified and mapped potentially intact lands across CONUS from 1986 to 2023 at 30 m resolution. We created three maps, first by applying a constant cultivation probability threshold across CONUS, second by varying the threshold state-by-state to maximize state-level overall accuracies, and third by equalizing the state-level user's and producer's accuracies to minimize classification bias. Validation against 800,000+ independent ground samples resulted in CONUS-level overall accuracies ≥85% for the roughly 660 million ha of potentially intact land. Map accuracy varied with the proportion of potentially intact lands across regions, with the Pacific-Mountain and Great Plains regions exhibiting the highest accuracies, while Eastern CONUS exhibited a greater mix of potentially intact and non-intact lands and more moderate map accuracies. These novel maps and approaches can be adapted to different spatiotemporal extents to support conservation and production decisions ranging from species and ecosystems protection to reducing land conversion and climate mitigation.

agriculture↗

Best practice reporting guideline for building stock energy models

Buildings are responsible for 38% of global greenhouse gas (GHG) emissions and, therefore, pathways to reduce their impact are crucial to achieve climate targets. Building stock energy models (BSEMs) have long been used as a tool to assess the current and future energy demand and environmental impact of building stocks. BSEMs have become more and more complex and are often tailored to case-specific datasets, which results in a high degree of heterogeneity among models. This heterogeneity, together with a lack of consistency in the reporting hinders the understanding of these models and, thereby, an accurate interpretation and comparison of results. In this paper we present a reporting guideline in order to improve reporting practices of BSEMs. The guideline was developed by experts as part of the IEA's Annex 70 and builds upon reporting guidelines from other fields. It consists of five topics (Overview, Model Components, Input and Output, Quality Assurance and Additional Information), which are further subdivided into subtopics. We explain which model aspects should be described in each subtopic, and provide illustrative examples on how to apply the guideline. In closing, the reporting guideline is consistent with the model classification framework and online model registry also developed in the Annex.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Field validation of data-driven BSDF and peak extraction models for light-scattering fabric shades

Shading and daylighting systems affect cooling, heating, and lighting energy use by modulating solar radiation through the building façade. Characterizing shading systems holistically and accurately helps designers and engineers evaluate shading systems to achieve energy and non-energy performance goals. These complex fenestration systems can be modeled using Bidirectional Scattering Distribution Functions (BSDF), which map incident radiation to hemispherical distributions of outgoing radiation. Data-driven, tabulated BSDFs are derived from interpolated goniophotometer measured data, then sampled during the raytracing calculation. A peak extraction (PE) algorithm was developed to circumvent limits in BSDF angular resolution, where the specular peak is extracted during simulation by evaluating the BSDF in the through direction and surrounding region. The objective of this study was to validate this measurement and modeling workflow using field monitored data from a full scale testbed with eleven installed fabrics of different weaves, openness factors, and colors and assess the accuracy of the workflow under different adaptation and contrast conditions. Test conditions were limited to clear sky conditions with the sun in the field of view. Results showed that, for tensor tree datasets, vertical illuminance, solar luminance (2.5° apex), and daylight glare probability (DGP) were predicted to within a mean bias error (MBE) error of -456 lx (-12.3%), -3.46e5 (-38.4%), and -0.042 (-7.8%) when full PE occurred. With a binary classification of glare/ no glare, DGP was predicted accurately with a true positive rate of 0.98 and true negative rate of 1.0 using tensor tree data and less accurately with Klems BSDF data, particularly for cases of no glare. The workflow may be of insufficient accuracy to distinguish borderline performance between fabrics using the four-point glare scale, particularly under low adaptation, high contrast daylit conditions. Errors were due to reductions in peak shape and intensity across the BSDF interpolation and data reduction workflow. Future work is needed to better preserve measurement fidelity during interpolation and sampling, which in turn will improve PE performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗