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At least 379 records · Page 21

Automated calculation and convergence of defect transport tensors

Defect diffusion is a key process in materials science and catalysis, but as migration mechanisms are often too complex to enumerate a priori, calculation of transport tensors typically have no measure of convergence and require significant end-user intervention. These two bottlenecks prevent high-throughput implementations essential to propagate model-form uncertainty from interatomic interactions to predictive simulations. In order to address these issues, we extend a massively parallel accelerated sampling scheme, autonomously controlled by Bayesian estimators of statewide sampling completeness, to build atomistic kinetic Monte Carlo models on a state-space irreducible under exchange and space group symmetries. Focusing on isolated defects, we derive analytic expressions for drift and diffusion coefficients, providing a convergence metric by calculating the Kullback–Leibler divergence across the ensemble of diffusion processes consistent with the sampling uncertainty. The autonomy and efficacy of the method is demonstrated on surface trimers in tungsten and Hexa-interstitials in magnesium oxide, both of which exhibit complex, correlated migration mechanisms.

36 MATERIALS SCIENCE↗

A Scalable Real-Time Data Assimilation Framework for Predicting Turbulent Atmosphere Dynamics

AI-based foundation models like FourCastNet, GraphCast are revolutionizing weather and climate predictions but are not yet ready for operational use. Their limitation lies in the absence of a data assimilation system to incorporate real-time Earth system observations, crucial for accurately forecasting events like tropical cyclones. To overcome these obstacles, we introduce a generic real-time data assimilation framework and demonstrate its end-to-end performance on the Frontier supercomputer. This framework comprises two primary modules: an ensemble score filter (EnSF), which significantly outperforms the state-of-the-art data assimilation method, and a vision transformer-based surrogate capable of real-time adaptation through the integration of observational data. We demonstrate both the strong and weak scaling of our framework up to 1024 GPUs on the Exascale supercomputer, Frontier. Our results not only illustrate the framework's exceptional scalability on high-performance computing systems, but also demonstrate the importance of supercomputers in real-time data assimilation for weather and climate predictions.

Lu, Dan↗

Data and scripts associated with the manuscript "Using Mutual Information for Global Sensitivity Analysis on Watershed Modeling"

This package contains the data and scripts used in "Using Mutual Information for Global Sensitivity Analysis on Watershed Modeling" (Jiang et al., 2022). The ARW_SWAT.zip file contains the SWAT simulation and the sensitivity analysis result in the American River Watershed. The Portage_SWAT.zip file contains the SWAT simulation and the sensitivity analysis result in the Portage River Watershed. The src folder contains the source code of sensitivity analysis and plotting functions. The notebooks folder contains the Jupyter notebooks for performing sensitivity analysis and other post analyses.Global Sensitivity Analysis (GSA) often is applied to assess the sensitivity of model outputs to their inputs using ensemble simulations. However, increasing model complexity and the associated computational cost have limited the use of most GSA approaches for process-based watershed models. We propose to use Mutual Information (MI) as a computationally efficient GSA method for watershed modeling. Such MI computed from several hundred realizations usually can capture nonlinear relationships between inputs and outputs of interest. We perform MI-based watershed sensitivity analyses in studies of the Portage River Watershed in Ohio and the American River Watershed in Washington. In these studies, MI is used to evaluate the sensitivity of river discharges simulated by the Soil and Water Assessment Tool to no less than 20 parameters for each watershed. Our MI-based sensitivity analyses achieved convergence with about 300~500 realizations, a small fraction of the ensemble size (i.e., several thousand) required by the Sobol method. Nevertheless, MI yields similar sensitivity ranking compared to the Sobol method, especially for sensitive parameters. Our study thus sheds new light on the use of MI as an affordable GSA method for computationally intensive models such as the hyper-resolution, watershed hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗

Representing Socio‐Economic Uncertainty in Human System Models

Abstract Socio‐economic development pathways and their implications for the environment are highly uncertain, and energy transitions will involve complex interactions among sectors. Here, traditional Monte Carlo analysis is paired with scenario discovery techniques to provide a richer portrait of these complexities. Modeled uncertain input variables include costs of advanced energy technologies, energy efficiency trends, fossil fuel resource availability, elasticities of substitution for labor, capital, and energy across economic sectors, population growth, and labor and capital productivity. The sampled values are simulated through a multi‐sector, multi‐region, recursively dynamic model of the world economy to explore a range of possible future outcomes. We find that many patterns of energy and technology development are possible for various long‐term environmental pathways and that sectoral output for most sectors is little affected through 2050 by the long‐term temperature target, but with tight constraints on emissions, emission intensities must fall much more rapidly. Scenario discovery techniques are applied to the large uncertainty ensembles to explore if there are prevailing storylines behind outcomes of interest. An illustrative investigation focused on different levels of economic growth shows many combinations of pathways and no single storyline emerging for a given economic outcome. This method can be extended to other outcomes of interest, exploring the nature of scenarios with both tail and median outcomes. Sampling from a Monte Carlo generated ensemble provides a rich set of scenarios to investigate, and potentially aids in avoiding heuristic biases in less structured scenario approaches.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Integrating multimodal data through interpretable heterogeneous ensembles

Motivation: Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems. Results: We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

59 BASIC BIOLOGICAL SCIENCES↗

FY21 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g., height, color and grayscale values; all as functions of a location in a plane projection). A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data, flag significant features, execute Machine Learning (ML) algorithms, output parameters for trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Features can be called out by user-specified thresholds, manual labeling or machine learning algorithms when they have been completed. The ability to rapidly label data is important because of the volume of data required for training machine learning algorithms. The GUI has the flexibility to allow addition of improved ML algorithms, methods for data visualization, and statistical computations. Statistical analyses via the GUI include areas of pits within a defined range of pit depths, correlations between Red-Green-Blue (RGB) or grayscale intensity and relative surface height, covariances between values associated with features, and feature histograms. The development of supervised machine learning algorithms, however, has been hindered by a lack of training data. The machine learning algorithms for crack identification are being refined but require improvements to the true positive rate for crack detection. This shortcoming is an artifact of the limited training data currently available, perhaps more so than the structure of the neural networks. At present, the best results are had from a consensus over an ensemble of randomly generated Deep Neural Network (DNN) or Convolutional Neural Network (CNN) algorithms. Although the consensus accuracy method has yielded optimum true positive and true negative rates in excess of 80%, additional validation testing is necessary. In addition to the suite of LCM data that was initially used, and which represents the majority of the work presented in this report, WAMS image data was also reviewed at a preliminary level. The review included a comparison between image resolution and dynamic range for each method. WAMS (ZON file) image data was found to have a pixel pitch of 3.69μm compared to 1 μm for the LCM (vk4 file) data, which implies a lower resolution for the WAMS images. Conversely, the ratio of dynamic range of the WAMS data to the LCM data was approximately 41:20 for height data, suggesting that information from WAMS should more accurately determine the depth of pits. At present, the significance of the greater dynamic range of the WAMS data relative to the LCM data has not yet been evaluated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Effective bands and band-like electron transport in amorphous solids

The localization of electrons caused by atomic disorder is a well-known phenomenon. However, under which circumstances electrons remain delocalized and retain band-like characteristics even when the crystal structure is completely absent, as found in certain amorphous solids, is less well understood. Here, in this study, to probe this phenomenon, we develop a fully first-principles description of the electronic structure and charge transport in amorphous materials, which combines a representation of the amorphous state as a composite (ensemble) of local environments and the state-of-the-art many-body electronic structure methods. Using amorphous In 2 O 3 as an example, we demonstrate the accuracy of our approach in reproducing the band-like nature of the conduction electrons as well as their disorder-limited mobility. Our approach reveals the physical origins responsible for the electron delocalization and survival of the band dispersions despite the absence of long-range order.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Realistic magnetic thermodynamics by local quantization of a semiclassical Heisenberg model

Abstract Classical Monte Carlo simulation of the Heisenberg model poorly describes many thermodynamic phenomena due to its neglect of the quantum nature of spins. Alternatively, we discuss how to semiclassically approach the quantum problem and demonstrate a simple method for introducing a locally approximate form of spin quantization. While the procedure underestimates magnetic short-range order, our results suggest a simple correction for recovering realistic spin–spin correlations above the critical temperature. Moreover, ensemble fluctuations are found to provide reasonably accurate thermodynamics, largely reproducing quantum mechanically calculated heat capacities and experimental magnetometry for ferromagnetic Fe and antiferromagnetic RbMnF 3 . Extensions of the method are proposed to address remaining inaccuracies.

36 MATERIALS SCIENCE↗

Cross-correlation spectra in interacting quantum dot systems

Two-color spin-noise spectroscopy of interacting electron spins in singly charged semiconductor quantum dots provides information on the interquantum dot interactions. We investigate the spin cross-correlation function in a quantum dot ensemble employing a modified semiclassical approach. Spin-correlation functions are calculated using a Hamilton quaternion approach that maintains local quantum mechanical properties of the spins. This method takes into account the effects of the nuclear-electric quadrupolar interactions, the randomness of the coupling constants, and the variation of the electron g factor on the spin-noise power spectra. We demonstrate that the quantum dot ensemble can be mapped on an effective two-quantum dot problem and discuss how the characteristic length scale of the interdot interaction modifies the low-frequency cross-correlation spectrum. Here, we argue that details on the interaction strength distribution can be extracted from the cross-correlation spectrum when applying a longitudinal or a transversal external magnetic field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Adapted Cell Design for the Operando X‑Ray Absorption Study of a Structurally Evolving Cu Nanoparticle Ensemble during the CO2 Electroconversion to Multicarbon Products

An improved understanding of the materials that will sustain the future of energy production, storage, and delivery calls for better characterization tools. Operando characterization methods have thus become essential for investigating electrocatalytic materials. Without their resulting insights, the study of highly performing catalysts post-mortem cannot viably facilitate the further development of functional catalysts. Herein, we present an operando electrochemical cell designed for hard X-ray absorption spectroscopy (XAS) and specifically adapted to the study of an electrocatalytically active Cu nanoparticle ensemble. So far, this nanocatalyst has proven to pose quite a challenge to characterize due to its unique structural dynamics. Adopting a design comparable to the H-cell employed for all activity testing, we report the satisfactory translation of the active site formation into an XAS-compatible cell. The simultaneous collection of CO2-derived products during XAS characterization enabled the operando characterization of this CO2-reducing active structure. We report a Cu–Cu coordination number of the first scattering path higher than suggested in our previous studies, highlighting the importance of monitoring metastable nanoelectrocatalysts in operando. This study illustrates important caveats for the electrocatalysis community when considering the application of operando XAS. Our results highlight that the sample size, homogeneity, and stability determine how to interpret the measured signal. Considering these parameters carefully, the operando EXAFS results confirm the exceptional undercoordinated character of the Cu nanoparticle ensemble during CO2 reduction to C2+ products.

Louisia, Sheena↗

An adaptive, data-driven multiscale approach for dense granular flows

The accuracy of coarse-grained continuum models of dense granular flows is limited by the lack of high-fidelity closure models for granular rheology. One approach to addressing this issue, referred to as the hierarchical multiscale method, is to use a high-fidelity fine-grained model to compute the closure terms needed by the coarse-grained model. The difficulty with this approach is that the overall model can become computationally intractable due to the high computational cost of the high-fidelity model. In this work, we describe a multiscale modeling approach for dense granular flows that utilizes neural networks trained using high-fidelity discrete element method (DEM) simulations to approximate the constitutive granular rheology for a continuum incompressible flow model. Our approach leverages an ensemble of neural networks to estimate predictive uncertainty that allows us to determine whether the rheology at a given point is accurately represented by the neural network model. Additional DEM simulations are only performed when needed, minimizing the number of additional DEM simulations required when updating the rheology. This adaptive coupling significantly reduces the overall computational cost of the approach while controlling the error. In addition, the neural networks are customized to learn regularized rheological behavior to ensure well-posedness of the continuum solution. We first validate the approach using two-dimensional steady-state and decelerating inclined flows. We then demonstrate the efficiency of our approach by modeling three-dimensional sub-aerial granular column collapse for varying initial column aspect ratios, where our multiscale method compares well with the computationally expensive computational fluid dynamics (CFD)-DEM simulation.

Dense granular flows↗

Catalytic Activity of an Ensemble of Sites for CO 2 Hydrogenation to Methanol on a ZrO 2 -on-Cu Inverse Catalyst

The significant increase in CO 2 emissions from heavy fossil fuel utilization has raised serious concerns, highlighting the need for effective methods to convert CO 2 into value-added chemicals. Here, in this work, we report a computational investigation on the catalytic activity of ZrO 2 -on-Cu inverse catalysts for CO 2 hydrogenation to methanol, considering highly dispersed ZrO 2 trimers on Cu (111). Such clusters present a large ensemble of formate-containing configurations, Zr 3 O n (OH) m (OCHO) l , making the evaluation of the catalytic activity very challenging. We found that the sites on the various catalyst configurations exhibit markedly different activities for formate hydrogenation, despite their similar free energy and composition. To understand these differences in reactivity, we examined the structural and electronic nature of the low free-energy catalyst configurations and identified that the energy of the lowest unoccupied orbital of the reacting formate, modified by its binding with the catalytic site, is a descriptor for the reaction energy of the formate hydrogenation step. From there, we screened an ensemble of catalyst structures using this descriptor to predict highly active metastable catalyst configurations and computed the reaction pathways and transition states for formate hydrogenation. From this investigation, we distinguished reactive from nonreactive sites and formate species on the ZrO 2 /Cu inverse catalyst based on structural and electronic features. We showed that rare metastable configurations control the activity. Additionally, an efficient method for examining the reactivity of a large number of coexisting catalyst structures was developed.

catalysts↗

MISPR : an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

36 MATERIALS SCIENCE↗

Characterization of Extremes and Compound Impacts: Applications of Machine Learning and Interpretable Neural Networks

Focal Area: This white paper responds to Focal area III by exploring data fusion, learning and explainable AI methods in characterizing hydrological extremes and interconnections. It also addresses Focal area II by using probabilistic AI and ensemble ML for predicting extremes and compound extremes. Science Challenge: A key question associated with the integrated water (or hydrological) cycle grand challenge in the Earth and Environmental Systems Sciences Division (EESSD) strategic plan, is how the frequency and intensity of hydrological events will change. Prediction of the tail behavior (extremes) of the hydrological cycle is especially challenging, because of their stochasticity and low probability. These extreme events and their compound impacts have significant societal and economic consequences. It is anticipated for the next-generation Earth System models (ESMs), that model predictability of the water cycle will improve with increased resolution (e.g., regionally refined E3SM), advanced software and computational architectures, and improved model physics based on the data from ARM measurements and high-fidelity models. However, the challenges for predictability of low-probability high-impact extreme events will unlikely be alleviated with conventional modeling and data-driven approaches, as ESMs are calibrated largely for capturing the high-frequency mean climate states. Recent AI and ML applications have shown great potential in quantifying well-defined climate extremes (e.g., supervised learning of tropical cyclones/atmospheric rivers by ClimateNet1) but few efforts are dedicated to compound events, extreme drivers and uncertainty estimation. We envision the opportunity to develop and apply ML and interpretable AI methods extended on the existing efforts, specifically, for: (1) identification of compound extremes, (2) diagnosing drivers of extremes, (3) bias correction in extreme predictions and (4) probabilistic modeling of extremes.

54 ENVIRONMENTAL SCIENCES↗

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping variations of redshift distributions with probability integral transforms

We present a method for mapping variations between probability distribution functions and apply this method within the context of measuring galaxy redshift distributions from imaging survey data. This method, which we name PITPZ for the probability integral transformations it relies on, uses a difference in curves between distribution functions in an ensemble as a transformation to apply to another distribution function, thus transferring the variation in the ensemble to the latter distribution function. This procedure is broadly applicable to the problem of uncertainty propagation. In the context of redshift distributions, for example, the uncertainty contribution due to certain effects can be studied effectively only in simulations, thus necessitating a transfer of variation measured in simulations to the redshift distributions measured from data. We illustrate the use of PITPZ by using the method to propagate photometric calibration uncertainty to redshift distributions of the Dark Energy Survey Year 3 weak lensing source galaxies. For this test case, we find that PITPZ yields a lensing amplitude uncertainty estimate due to photometric calibration error within 1 per cent of the truth, compared to as much as a 30 per cent underestimate when using traditional methods.

79 ASTRONOMY AND ASTROPHYSICS↗

Matrix Approach to Accelerate Spin-Up of CLM5

Numerical models have been developed to investigate and understand responses of biogeochemical cycle to global changes. Steady state, when a system is in dynamic equilibrium, is generally required to initialize these model simulations. However, the spin-up process that is used to achieve steady state pose a great burden to computational resources, limiting the efficiency of global modeling analysis on biogeochemical cycles. This study introduces a new Semi-Analytical Spin-Up (SASU) to tackle this grand challenge. We applied SASU to Community Land Model version 5 and examined its computational efficiency and accuracy. At the Brazil site, SASU is computationally 7 times more efficient than (or saved up to 86% computational cost in comparison with) the traditional native dynamics (ND) spin-up to reach the same steady state. Globally, SASU is computationally 8 times more efficient than the accelerated decomposition spin-up and 50 times more efficient than ND. In summary, SASU achieves the highest computational efficiency for spin-up on site and globally in comparison with other spin-up methods. It is generalizable to wide biogeochemical models and thus makes computationally costly studies (e.g., parameter perturbation ensemble analysis and data assimilation) possible for a better understanding of biogeochemical cycle under climate change.

54 ENVIRONMENTAL SCIENCES↗

27 AlNMR chemical shift of Al(OH)$^{-}_{4}$ calculated from first principles: Assessment of error cancellation in chemically distinct reference and target systems

Predicting accurate nuclear magnetic resonance chemical shieldings relies upon cancellation of different types of errors between the theoretically calculated shielding constant of the analyte of interest and the reference. Often, the intrinsic error in computed shieldings due to basis sets, approximations in the Hamiltonian, description of the wave function, and dynamic effects is nearly identical between the analyte and reference, yet if the electronic structure or sensitivity to local environment differs dramatically, this cannot be taken for granted. Detailed prior work has examined the octahedral trivalent cation Al(H 2 O)$^{3+}_{6}$, accounting for ab initio intrinsic errors. However, the use of this species as a reference for the chemically distinct tetrahedral anion Al(OH)$^{-}_{4}$ requires an understanding of how these errors cancel, in order to define the limits of accurately predicting 27 Al chemical shielding in Al(OH)$^{-}_{4}$. In this work, we estimate the absolute shielding of the 27 Al nucleus in Al(OH)$^{-}_{4}$ at the coupled cluster level (515.1± 5.3 ppm). Shielding sensitivity to the choice of method approximation and atomic basis sets used has been evaluated. Solvent and thermal effects are assessed through ensemble averaging techniques using ab-initio molecular dynamics. The contribution of each type of intrinsic error is assessed for the Al(H 2 O)$^{3+}_{6}$ and Al(OH)$^{-}_{4}$ ions, revealing significant differences that fundamentally hamper the ability to accurately calculate the 27 Al chemical shift of Al(OH)$^{-}_{4}$ from first principles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗