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At least 217 records · Page 12

An uncertainty visualization framework for large-scale cardiovascular flow simulations: A case study on aortic stenosis

We present a generalizable uncertainty quantification (UQ) and visualization framework for lattice Boltzmann method simulations of high Reynolds number vascular flows, demonstrated on a patient-specific stenosed aorta. The framework combines EasyVVUQ for parameter sampling with large-eddy simulation turbulence modeling in HemeLB, and executes ensembles on the Frontier exascale supercomputer. Spatially resolved metrics, including entropy and isosurface-crossing probability, are used to map uncertainty in pressure and wall shear stress fields directly onto vascular geometries. Two sources of model variability are examined: inlet peak velocity and the Smagorinsky constant. Inlet velocity variation produces high uncertainty downstream of the stenosis where turbulence develops, while upstream regions remain stable. Smagorinsky constant variation has little effect on the large-scale pressure field but increases WSS uncertainty in localized high-shear regions. In both cases, the stenotic throat manifests low entropy, indicative of robust identification of elevated WSS. By linking quantitative UQ measures to three-dimensional anatomy, the framework improves interpretability over conventional 1D UQ plots and supports clinically relevant decision-making, with broad applicability to vascular flow problems requiring both accuracy and spatial insight.

Hemodynamics↗

Bayesian learning for rapid prediction of lithium-ion battery-cycling protocols

Advancing lithium-ion battery technology requires the optimization of cycling protocols. A new data-driven methodology is demonstrated for rapid, accurate prediction of the cycle life obtained by new cycling protocols using a single test lasting only 3 cycles, enabling rapid exploration of cycling protocol design spaces with orders of magnitude reduction in testing time. We achieve this by combining lifetime early prediction with a hierarchical Bayesian model (HBM) to rapidly predict performance distributions without the need for extensive repetitive testing. The methodology is applied to a comprehensive dataset of lithium-iron-phosphate/graphite comprising 29 different fast-charging protocols. HBM alone provides high protocol-lifetime prediction performance, with 6.5% of overall test average percent error, after cycling only one battery to failure. Here, by combining HBM with a battery lifetime prediction model, we achieve a test error of 8.8% using a single 3-cycle test. In addition, the generalizability of the HBM approach is demonstrated for lithium-manganese-cobalt-oxide/graphite cells.

25 ENERGY STORAGE↗

Non-DNA radiosensitive targets that initiate persistent behavioral deficits in rats exposed to space radiation

Predicting future CNS risks for astronauts during deep-space missions will rely substantially on ground-based rodent data with space-relevant ions and behaviors. For rats, the accumulated evidence indicates that less densely ionizing radiation, such as 4 He and 12 C ions, induce behavior deficits at lower doses than densely ionizing ions, such as 48 Ti and 56 Fe. However, this observation conflicts with standard somatic radiobiology, in which densely ionizing ions are generally more effective than less densely ionizing ions, and where the DNA/nucleus is the accepted target for radiation-induced tumorigenesis, cytogenetic aberrations, genetic mutations, and reproductive cell death. To gain deeper insight into the subcellular nature of the radiation targets for behavior risks, we compared the effects of dose, fluence, and linear energy transfer (LET) of 4 He and 56 Fe particles using existing datasets for four distinct behavioral outcomes in rats: elevated plus maze (EPM-anxiety), novel object recognition (NOR-memory), operant responding (OR-response to environmental stimuli), and attentional set-shifting (ATSET-cognitive flexibility). We confirmed that less densely ionizing particles (except protons) showed ~100-fold lower threshold doses than densely ionizing particles for behavioral deficits (0.1–1 cGy for 4 He vs. 15–100 cGy for 56 Fe). However, when analyzed by fluence the behavioral responses converged, indicating that 4 He and 56 Fe were equally effective on a per-track basis. When analyzed by LET, there were ~100-fold differences in the LET for maximum effectiveness for behavioral deficits and DNA endpoints (~1 vs ~100 keV/μm, respectively). These unique features of radiation-induced behavioral deficits (high sensitivity to particles in the 1-keV/μm range, insensitivity to protons in the 0.2 keV/μm range, and isofluence dependence for particles with LET>1 keV/μm) provide evidence in support of a new hypothesis of sub-micron sized radiosensitive targets for behavioral effects consistent with the thickness of plasma membranes and/or small subcellular structures, smaller than a whole synapse. Like our behavior findings, mouse immature oocyte killing which is known to have a plasma membrane target was also better explained by fluence, rather than dose. In contrast, fluence analyses for DNA/nuclear endpoints in somatic cells (e.g., tumor induction, chromosome aberrations) showed opposite results, suggesting that behavior targets are not DNA. Our findings raise questions regarding the identity of subcellular targets and the multi-cellular functional unit for behavior risks, low-dose susceptibility, and generalizability from rat to other species and astronauts.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Modular multi-interface nanocrystals for enhanced ethanol oxidation electrocatalysis

Electrochemical processes that utilize biomass-derived ethanol as a source of electrons and protons offer a sustainable energy strategy, yet their practical implementation is limited by sluggish ethanol oxidation reaction (EOR) kinetics and catalyst poisoning. Here, in this study, we report a modular multi-interface nanocrystal catalyst comprising core/shell Co 2 P/Pd and Pd-Au heterostructured interfaces that exhibit complementary functions for the enhanced EOR catalysis. The Co 2 P/Pd interface boosts Pd atom utilization and lowers the kinetic barriers for ethanol-to-acetate conversion, while the Pd-Au interface effectively alleviates CO poisoning caused by C–C bond cleavage of ethanol. In-depth analyses using in situ attenuated total reflectance-surface-enhanced infrared absorption spectroscopy, differential electrochemical mass spectrometry, and density functional theory calculations elucidate the mechanistic roles of these interfaces. The optimized Co 2 P/Pd-Au 0.08 nanorods achieve an excellent mass activity, underscoring the potential of modular, multi-interface nanocrystals for advancing EOR catalysis and offering a generalizable strategy for broader catalytic innovations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Machine learning prediction on the fractional free volume of polymer membranes

Fractional free volume (FFV) characterizes the microstructural level features of polymers and affects their properties including thermal, mechanical, and separation performance. Experimental measurements and theoretical analyses have been used to quantify the FFV of polymers, but challenges remain because of their limitations. Experimental measurements are laborious and based on semi empirical equations, while Bondi’s group contribution theory involves ambiguities like the determination of van der Waals volume and the choice of factor values in the theoretical equation. To efficiently evaluate the FFV of polymers, this study utilizes high-throughput molecular dynamics (MD) simulations to build a large dataset regarding polymer’s FFV. Based on this large dataset, we further build machine learning (ML) models to establish the composition-structure relation. Inspired by group contribution theory which correlates polymer’s functional groups to FFV, our ML models correlate polymer’s substructures or physico-chemical indexes to FFV. Here, our study first benchmarks the MD simulation protocol to obtain reliable FFV of polymers and then carries out high-throughput MD simulations for more than 6,500 homopolymers and 1,400 polyamides. Such a large and diverse dataset makes the well-trained ML models more generalizable, compared with the group contribution theory. The efficiency of a feed forward neural network model is further demonstrated by applying it to a hypothetical polyimide dataset of more than 8 million chemical structures. The predicted FFVs of hypothetical polyimides are further validated by MD simulations. The obtained FFVs of the 8 million polymers, plus their previously reported gas separation performances, demonstrate the promising capability of ML virtual screening for the discovery of polymer membranes with exceptional permeability/selectivity.

36 MATERIALS SCIENCE↗

Tapping the treasure trove of atypical phages

With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncovered from different ecosystems. Though these efforts have revealed the existence and prevalence of these nonmodel phages, computational approaches often fail to associate these phages with their specific bacterial host(s), while the lack of methods to isolate these phages has limited our ability to characterize infectivity pathways and new gene function. In this review, we call for the development of generalizable experimental methods to better capture this understudied viral diversity via isolation and study them through gene-level characterization and engineering. Establishing a diverse set of new ‘atypical’ phage model systems has the potential to provide many new biotechnologies, including potential uses of these atypical phages in halting the spread of antibiotic resistance and engineering of microbial communities for beneficial outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

Levenberg–Marquardt multi-classification using hinge loss function

Incorporating higher-order optimization functions, such as Levenberg-Marquardt (LM) have revealed better generalizable solutions for deep learning problems. However, these higher-order optimization functions suffer from very large processing time and training complexity especially as training datasets become large, such as in multi-view classification problems, where finding global optima is a very costly problem. To solve this issue, we develop a solution for LM-enabled classification with, to the best of knowledge first-time implementation of hinge loss, for multiview classification. Hinge loss allows the neural network to converge faster and perform better than other loss functions such as logistic or square loss rates. Here we prove our method by experimenting with various multiclass classification challenges of varying complexity and training data size. The empirical results show the training time and accuracy rates achieved, highlighting how our method outperforms in all cases, especially when training time is limited. Our paper presents important results in the relationship between optimization and loss functions and how these can impact deep learning problems.

97 MATHEMATICS AND COMPUTING↗

Predicting material microstructure evolution via data-driven machine learning

The recent rapid rise in data-driven practices in the materials science domain has led to the development of efficient, generalizable, and accurate approaches for several applications, including: material property prediction, mining (micro)structure- property and (micro)structure-processing relationships, and characterization of material microstructures. Central to the materials science domain is linking microstructure to properties and performance, and critical to building such linkages is understanding how microstructures evolve as a function of environmental exposure or processing conditions (e.g., time, temperature, applied stress or strain, irradiation). This preview article summarizes recent work on the development of recurrent neural networks for predicting spatio-temporal microstructure evolution detailed by Yang et al in their manuscript entitled 'Self-supervised Learning and Prediction of Microstructure Evolution with Recurrent Neural Networks'.

machine learning (ML), materials characterization↗

Universal machine learning framework for defect predictions in zinc blende semiconductors

Our article introduces a universal predictive framework for point defect formation energies and charge transition levels in a wide chemical space of zinc blende semiconductors and possible impurity atoms selected from across the periodic table. This framework was developed by leveraging high-throughput quantum mechanical simulations benchmarked using some experimental data from the literature, as well as machine learning (ML)-based regressions techniques that map unique materials descriptors to computed defect properties and yield optimized and generalizable models. Furthermore, the power and utility of these models is revealed through quick predictions for thousands of new defects and screening of low-energy impurities, which may tune the equilibrium conductivity in the semiconductor. This work presents, to our knowledge, the largest density functional theory (DFT) dataset of defect properties in semiconductors and the largest DFT+ML-based screening of point defects in semiconductors to date.

36 MATERIALS SCIENCE↗

Frame invariant neural network closures for Kraichnan turbulence

Numerical simulations of geophysical and atmospheric flows have to rely on parameterizations of subgrid scale processes due to their limited spatial resolution. Despite substantial progress in developing parameterization (or closure) models for subgrid scale (SGS) processes using physical insights and mathematical approximations, they remain imperfect and can lead to inaccurate predictions. In recent years, machine learning has been successful in extracting complex patterns from high-resolution spatio-temporal data, leading to improved parameterization models, and ultimately better coarse grid prediction. However, the inability to satisfy known physics and poor generalization hinders the application of these models for real-world problems. In this work, we put forth a frame invariant closure approach to improve the accuracy and generalizability of deep learning-based subgrid scale closure models by embedding physical symmetries directly into the structure of the neural network. Specifically, we utilized specialized layers within the convolutional neural network in such a way that desired constraints are theoretically guaranteed without the need for any regularization terms. We demonstrate our framework for a two-dimensional decaying turbulence test case mostly characterized by the forward enstrophy cascade. We show that our frame invariant SGS model (i) accurately predicts the subgrid scale source term, (ii) respects the physical symmetries such as translation, Galilean, and rotation invariance, and (iii) is numerically stable when implemented in coarse-grid simulation with generalization to different initial conditions and Reynolds number. This work opens up a possibility of connecting physics-based theories and data-driven modeling paradigms, and thus represents a promising step towards the development of physically consistent data-driven turbulence closure models.

42 ENGINEERING↗

Lift & Learn: Physics-informed machine learning for large-scale nonlinear dynamical systems

In this work, we present Lift & Learn, a physics-informed method for learning low-dimensional models for large-scale dynamical systems. The method exploits knowledge of a system’s governing equations to identify a coordinate transformation in which the system dynamics have quadratic structure. This transformation is called a lifting map because it often adds auxiliary variables to the system state. The lifting map is applied to data obtained by evaluating a model for the original nonlinear system. This lifted data is projected onto its leading principal components, and low-dimensional linear and quadratic matrix operators are fit to the lifted reduced data using a least-squares operator inference procedure. Analysis of our method shows that the Lift & Learn models are able to capture the system physics in the lifted coordinates at least as accurately as traditional intrusive model reduction approaches. This preservation of system physics makes the Lift & Learn models robust to changes in inputs. Numerical experiments on the FitzHugh–Nagumo neuron activation model and the compressible Euler equations demonstrate the generalizability of our model.

97 MATHEMATICS AND COMPUTING↗

Assessments of epistemic uncertainty using Gaussian stochastic weight averaging for fluid-flow regression

Here, we use Gaussian stochastic weight averaging (SWAG) to assess the epistemic uncertainty associated with neural-network-based function approximation relevant to fluid flows. SWAG approximates a posterior Gaussian distribution of each weight, given training data, and a constant learning rate. Having access to this distribution, it is able to create multiple models with various combinations of sampled weights, which can be used to obtain ensemble predictions. The average of such an ensemble can be regarded as the 'mean estimation', whereas its standard deviation can be used to construct 'confidence intervals', which enable us to perform uncertainty quantification (UQ) with regard to the training process of neural networks. We utilize representative neural-network-based function approximation tasks for the following cases: (i) a two-dimensional circular-cylinder wake; (ii) the DayMET dataset (maximum daily temperature in North America); (iii) a three-dimensional square-cylinder wake; and (iv) urban flow, to assess the generalizability of the present idea for a wide range of complex datasets. SWAG-based UQ can be applied regardless of the network architecture, and therefore, we demonstrate the applicability of the method for two types of neural networks: (i) global field reconstruction from sparse sensors by combining convolutional neural network (CNN) and multi-layer perceptron (MLP); and (ii) far-field state estimation from sectional data with two-dimensional CNN. We find that SWAG can obtain physically-interpretable confidence-interval estimates from the perspective of epistemic uncertainty. This capability supports its use for a wide range of problems in science and engineering.

97 MATHEMATICS AND COMPUTING↗

Fourier-MIONet: Fourier-enhanced multiple-input neural operators for multiphase modeling of geological carbon sequestration

Geologic carbon sequestration (GCS) is a safety-critical technology that aims to reduce the amount of carbon dioxide in the atmosphere, which also places high demands on reliability. Multiphase flow in porous media is essential to understand CO 2 migration and pressure fields in the subsurface associated with GCS. However, numerical simulation for such problems in 4D is computationally challenging and expensive, due to the multiphysics and multiscale nature of the highly nonlinear governing partial differential equations (PDEs). It prevents us from considering multiple subsurface scenarios and conducting real-time optimization. Here, we develop a Fourier-enhanced multiple-input neural operator (Fourier-MIONet) to learn the solution operator of the problem of multiphase flow in porous media. Fourier-MIONet utilizes the recently developed framework of the multiple-input deep neural operators (MIONet) and incorporates the Fourier neural operator (FNO) in the network architecture. Once Fourier-MIONet is trained, it can predict the evolution of saturation and pressure of the multiphase flow under various reservoir conditions, such as permeability and porosity heterogeneity, anisotropy, injection configurations, and multiphase flow properties. Compared to the enhanced FNO (U-FNO), the proposed Fourier-MIONet has 90% fewer unknown parameters, and it can be trained in significantly less time (about 3.5 times faster) with much lower CPU memory (<15%) and GPU memory (<35%) requirements, to achieve similar prediction accuracy. In addition to the lower computational cost, Fourier-MIONet can be trained with only 6 snapshots of time to predict the PDE solutions for 30 years. Furthermore, we observed that Fourier-MIONet can maintain good accuracy when predicting out-of-distribution (OOD) data. The excellent generalizability of Fourier-MIONet is enabled by its adherence to the physical principle that the solution to a PDE is continuous over time. Furthermore, the developed Fourier-MIONet makes it possible to solve the long-time evolution of geological carbon sequestration in a large-scale three-dimensional space accurately and efficiently.

97 MATHEMATICS AND COMPUTING↗

A new framework to map fine resolution cropping intensity across the globe: Algorithm, validation, and implication

We report accurate estimation of cropping intensity (CI), an indicator of food production, is well aligned with the ongoing efforts to achieve sustainable development goals (SDGs) under diminishing natural resources. The advancement in satellite remote sensing provides unprecedented opportunities for capturing CI information in a spatially continuous manner. However, challenges remain due to the lack of generalizable algorithms for accurately and efficiently mapping global CI with a fine spatial resolution. In this study, we developed a 30-m planetary-scale CI mapping framework with the reconstructed time series of Normalized Difference Vegetation Index (NDVI) from multiple satellite images. Using a binary crop phenophase profile indicating growing and non-growing periods, we estimated pixel-by-pixel CI by enumerating the total number of valid cropping cycles during the study years. Based on the Google Earth Engine cloud computing platform, we implemented the framework to estimate CI during 2016–2018 in eight geographic regions across continents that are representative of global cropping system diversity. Comparison with PhenoCam network data in four cropland sites suggests that the proposed framework is capable of capturing the seasonal dynamics of cropping practices. Spatially, overall accuracies based on validation samples range from 80.0% to 98.9% across different regions worldwide. Regarding the CI classes, single cropping systems are associated with more robust and less biased estimations than multiple cropping systems. Finally, our CI estimates reveal high agreement with two widely used land surface phenology products, including Vegetation Index and Phenology V004 (VIP4) and Moderate Resolution Imaging Spectroradiometer Land Cover Dynamics (MCD12Q2), meanwhile providing much more spatial details. Due to its robustness, the developed CI framework can be potentially generalized to produce global fine resolution CI products for food security and other applications.

54 ENVIRONMENTAL SCIENCES↗

An adaptive synchronous extraction (ASE) method for estimating intensity and footprint of surface urban heat islands: A case study of 254 North American cities

The urban heat island (UHI) effect has attracted great attention due to its potential impacts on rapidly growing urban areas. Using remotely sensed estimates of land surface temperature (LST), a large number of studies have focused on the surface UHI (SUHI) effect, which can be characterized by its two fundamental properties: intensity and footprint. The SUHI intensity reflects the LST difference between the urban area and the background reference area (BRA), and the SUHI footprint indicates the spatial extent influenced by the heat island. Currently, numerous methods have been developed to estimate the SUHI intensity and footprint, but are still greatly challenged by three main issues. Namely, the discrepancy in BRA selection criterion brings great uncertainty to the estimated SUHI intensity, the estimation of SUHI footprint is largely constrained by the predefined models, and the quantification of SUHI effect is potentially influenced by several confounding factors. Here, we proposed an adaptive synchronous extraction (ASE) method, which is capable of adaptively selecting the most optimal BRA while removing the influence of confounding factors, and achieving synchronous estimation of SUHI intensity and footprint. We applied the ASE method to 254 North American cities and conducted an in-depth comparative analysis to discuss its applicability and benefits. The main results include: (1) The ASE method avoids the limitations of existing methods in BRA selection and model presetting, and shows resilience to parameter variations. This makes the ASE method highly applicable to quantify the SUHI intensity and footprint in cities with various thermal characteristics. (2) The ASE method can better highlight the spatial, seasonal and day-night contrasts in the estimated SUHI intensity. This superiority is particularly evident when comparing it to methods based on the equal-area buffer or the simplified urban-extent algorithm. (3) Confounding factors pose non-negligible impacts on the quantification of the SUHI effect. Typically, ignoring the influence of topographic relief or missing LST data can lead to an overall overestimation of the SUHI intensity, while not removing surrounding urban areas will cause some underestimation of the SUHI intensity. In conclusion, overall, the proposed ASE method provides a new generalizable tool for quantifying the SUHI effect, which has great potentials for future studies and urban climate assessments.

54 ENVIRONMENTAL SCIENCES↗

Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

Stream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed ‘meta-metabolome ecology.’ Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering and variations in putative biochemical transformations. We refer to this phenomenon as ‘thermodynamic redundancy,’ which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

Danczak, Robert E.↗

Autonomous alloy composition optimization using molecular dynamics guided by a large language model

Here, we present an autonomous materials discovery framework that couples a large language model (LLM) with molecular dynamics (MD) simulations to optimize Fe–Cr–Mn alloy compositions for tensile strength. Starting from six distinct compositions, the LLM operated as an intelligent agent, iteratively proposing changes based on prior simulation results and constraints. Over 50 iterations per case, the LLM adaptively explored the composition space, identifying high-strength regions, not easily accessible by conventional methods. The highest strength, 18.7 GPa, was achieved with Fe 71 Cr 25 Mn 4 composition, identified from a Fe 75 Cr 20 Mn 5 starting point. The LLM autonomously adjusted its strategy in real time, demonstrating closed-loop decision-making using commodity hardware. This approach showcases the potential of LLMs as scientific co-pilots, capable of accelerating materials discovery and generalizable to other domains like biology and drug design.

Autonomy↗

Revisiting diffusion-based moisture functions: why do they fail?

Microbial activities in soil are controlled by the balance between physical and biological mechanisms that are currently implied by soil moisture-respiration relationships, but not explicitly represented. Diffusion based moisture functions focus on physical controls, while substrate kinetics based models primarily address biological drivers. How to harmonize these two types of models for robust predictions of soil respiration and other processes has not been addressed. Here we derived a generalizable analytical solution of diffusion-limited nonlinear microbial uptake kinetics, in which microbial metabolic rates were governed by both physical and biological drivers via substrate diffusion and microbial affinity. We proposed a soil trait concept to integrate both physical and biological perspectives into one unified function, and tested it using both laboratory and field based observations from a variety of soils. This approach provides a tractable and scalable approach that incorporates soil heterogeneity and functional complexity in macroscopic model descriptions.

59 BASIC BIOLOGICAL SCIENCES↗