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At least 73 records · Page 4

Conformational ensembles reveal the origins of serine protease catalysis

Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. In conclusion, our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.

Du, Siyuan [Stanford Univ., CA (United States)] (O↗

Implementation of stacked ensemble machine learning for the detection of surrogate plutonium contamination in soil via LIBS

Supervised machine learning methods have demonstrated increased utility for the quantification of lanthanide and actinide elements in atomic spectroscopy applications. This study implements laser-induced breakdown spectroscopy (LIBS) for the identification of plutonium surrogate material (CeO 2 ) in soil matrices by training supervised machine learning methods on the recorded spectral data. A bagged ensemble using Random Forest yields the highest sensitivity predictions with a detection limit of 0.015 wt.% CeO 2 . However, high precision in Ce content prediction required the use of a stacked ensemble regression, which provided the superlative Ce quantification model with an error of 0.107% and a detection limit of 0.022 wt.%. Furthermore, the high performance of the stacked ensemble demonstrates its potential to enhance the accuracy and sensitivity of nuclear contaminant detection using field-deployable spectroscopic analyzers in real-world scenarios.

47 OTHER INSTRUMENTATION↗

Ensemble Simulation Techniques and Fast Randomized Algorithms

The major goals of the project were to develop and analyze new ensemble simulation techniques, including trajectory stratification and preconditioned MCMC techniques, as well as develop fast numerical linear algebra techniques closely related to ensemble simulation ideas. The trajectory stratification techniques involve simulating in parallel short trajectory fragments of a Markov process confined to a specific region of space‐time and then patching together the statistics gathered to assemble estimates of very general dynamical properties. We have also developed this approach for rare event simulation and extended the techniques to applications requiring a more general framework (such as electronic structure calculations). The preconditioned MCMC techniques involve simulating multiple Markov chains in parallel and then using information from the ensemble to speed the mixing of each individual chain. The fast randomized linear algebra methods are motivated by the diffusion Monte Carlo technique, but are applicable to finding the dominant eigenvalue of (almost) general matrices. For most non‐negative matrices, the schemes result in an error (compared to the power method) that is constant in the dimension of the problem. For more general matrices, we see a very clear sublinear cost trend in computational tests.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Plateau to River Model Predictive Simulations for All Ensemble Realizations to Support Modeling Work in Fiscal Year 2025

The purpose of this environmental calculation file (ECF) is to document predictions of flow and hydraulic head on the Central Plateau of the Hanford Site using the Plateau-to-River (P2R) Model (CP-57037, Model Package Report for the Plateau-to-River Model: Version 9.1). This calculation documents the simulation of the groundwater for the parent model domain of the P2R Model as a basis for use in other applications of the P2R Model. This application is unique from the standpoint that it will simulate all ensemble member models of the P2R Model whereas other applications may only utilize specific ensemble members. These simulations provide results that can be used in the process of selecting an appropriate subset of ensemble members for other applications.

54 ENVIRONMENTAL SCIENCES↗

Workflows for Science: A comprehensive guide for ensemble workflow tools usage with applications on OLCF systems

The growing demand for robust computational and workflow environments for scientific applications and user communities at the Oak Ridge Leadership Computing Facility (OLCF) has prompted collaboration with ensemble tools development teams and facility users to produce this technical paper. We connect science applications to the RADICAL-Pilot (RP) workflow tool to execute ensemble instantiations using the Frontier supercomputer. The documented installation, usage, and execution demonstrates how RP streamlines scientific workflows at OLCF. We outline the specific steps OLCF users can follow to integrate this tool with their applications and advance their research. This document stands as a comprehensive guide to OLCF users of ensemble workflow tools with examples on real applications using the Frontier supercomputer.

97 MATHEMATICS AND COMPUTING↗

Uncertainty based Online Ensemble on Non-Stationary Data for Fusion Science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior due to drifts in the data. The drifts can arise from both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with non-stationary data streams.Online learning can be used to continuously adapt the models with new data as it is acquired. However, traditional online learning can suffer from short-term performance degradation, as ground truth are not available before making the prediction. To address this challenge, we propose uncertainty aware ensemble approach for online learning. We use Deep Gaussian Process Approximation (DGPA) technique for calibrated uncertainty estimation and use the uncertainty values to guide a meta-algorithm that produces predictions based on ensemble of learners. Moreover, DGPA also provides uncertainty estimation along with the predictions for decision makers. This paper demonstrates that the proposed method outperforms traditional online learning approach, and a naive ensemble without uncertainty guidance by about 7% and 6%, respectively, on B-coil deflection prediction at DIII-D Fusion Facility.

Rajput, Kishansingh [Thomas Jefferson National Acc↗

Synthetic Atmospheric River Ensembles Generated by Deep-AR

This dataset contains 35,850 synthetic landfalling atmospheric river (AR) realizations generated by the Deep-AR two-stage deep-learning framework over the Northeast Pacific and U.S. West Coast. The archive contains 25 stochastic ensemble members for each of 1,434 held-out observed seed events. Each synthetic realization is initialized from conditions 48 hours before the corresponding observed AR landfall and is generated autoregressively at 6-hour intervals over a 144-hour period. Deep-AR combines a deterministic residual network (ResNet) that advances the large-scale atmospheric state with a Wasserstein generative adversarial network (WGAN) that produces stochastic, high-resolution fields. Each HDF5 file contains 0.25° gridded synthetic integrated vapor transport components (qu, qv), 10 m wind components (u10, v10), and 6-hour accumulated precipitation on a common 200 × 480 grid. The files also include coordinate and datetime arrays. This dataset supports AR hazard analysis, ensemble-based uncertainty characterization, precipitation-extremes research, and regional stress testing. Synthetic files follow the naming convention deepar.model.YYYYMMDD.HHMMSS.vNN.h5. YYYYMMDD.HHMMSS identifies the UTC initial-condition timestamp, which occurs 48 hours before the diagnosed observed landfall, and vNN identifies the zero-padded ensemble member, ranging from v01 through v25. Each synthetic file can be paired with its corresponding observed file by matching the initial-condition timestamp. The paired observed file follows the naming convention deepar.obs.YYYYMMDD.HHMMSS.h5 and is available in the separately registered oracle/deepar.obs dataset at https://wdh.energy.gov/ds/oracle/deepar.obs (DOI: https://doi.org/10.21947/3377671).

17 WIND ENERGY↗

Uncertainty based Online Ensemble on Non-Stationary Data for Fusion Science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior due to drifts in the data. The drifts can arise from both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with non-stationary data streams.Online learning can be used to continuously adapt the models with new data as it is acquired. However, traditional online learning can suffer from short-term performance degradation, as ground truth are not available before making the prediction. To address this challenge, we propose uncertainty aware ensemble approach for online learning. We use Deep Gaussian Process Approximation (DGPA) technique for calibrated uncertainty estimation and use the uncertainty values to guide a meta-algorithm that produces predictions based on ensemble of learners. Moreover, DGPA also provides uncertainty estimation along with the predictions for decision makers. This paper demonstrates that the proposed method outperforms traditional online learning approach, and a naive ensemble without uncertainty guidance by about 7% and 6%, respectively, on B-coil deflection prediction at DIII-D Fusion Facility.

Rajput, Kishansingh [Thomas Jefferson National Acc↗

Enhanced accuracy through ensembling of randomly initialized auto-regressive models for dynamical systems

Computational mechanics simulations using traditional finite element methods (FEM) require prohibitively expensive computational resources for real-time engineering applications, design optimization, and digital twin implementations. While machine learning (ML) surrogate models offer significant computational speedups, autoregressive ML models for time-dependent mechanical systems suffer from error accumulation that compromises long-term prediction reliability - a critical concern for engineering applications where accuracy over extended time horizons is essential for safety and performance assessments. Here, we propose a deep ensemble framework specifically designed to address this challenge in computational mechanics applications, where multiple ML surrogate models with random weight initializations are trained in parallel and their predictions aggregated during inference. This approach leverages statistical diversity to maximize information gain from a fixed set of training data and to mitigate error propagation, while maintaining the computational efficiency that makes ML surrogates attractive for engineering practice. We validate the framework on three representative problems spanning critical areas of computational mechanics: stress field evolution in heterogeneous microstructures under complex loading (relevant to advanced materials design and composite analysis), planetary-scale shallow water dynamics (applicable to environmental and geotechnical engineering), and Gray-Scott reaction-diffusion systems (relevant to mass transport and chemical process engineering). Across all test cases, the ensemble approach demonstrates consistent error reduction of 15-33% compared to individual models. The codes for this work are available on GitHub (https://github.com/Graham-Brady-Research-Group/AutoregressiveEnsemble_SpatioTemporal_Evolution).

autoregressive prediction↗

Approaching periodic systems in ensemble density functional theory via finite one-dimensional models

Ensemble density functional theory (EDFT) is a generalization of ground-state DFT, which is based on an exact formal theory of finite collections of a system's ground and excited states. EDFT in various forms has been shown to improve the accuracy of calculated energy level differences in isolated model systems, atoms, and molecules, but it is not yet clear how EDFT could be used to calculate band gaps for periodic systems. We extend the application of EDFT toward periodic systems by estimating the thermodynamic limit with increasingly large finite one-dimensional 'particle in a box' systems, which approach the uniform electron gas (UEG). Using ensemble-generalized Hartree and local spin density approximation exchange-correlation functionals, we find that corrections go to zero in the infinite limit, as expected for a metallic system. However, there is a correction to the effective mass, with results comparable to other calculations on 1D, 2D, and 3D UEGs, which indicates promise for non-trivial results from EDFT on periodic systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Learning and discovering multiple solutions using physics-informed neural networks with random initialization and deep ensemble

In this work we explore the capability of physics-informed neural networks (PINNs) to discover multiple solutions. Many real-world phenomena governed by nonlinear differential equations (DEs), such as fluid flow, exhibit multiple solutions under the same conditions, yet capturing this solution multiplicity remains a significant challenge. A key difficulty lies in providing appropriate initial conditions or guesses, as widely used time-marching schemes and Newton’s method are highly sensitive to these choices when solving complex computational problems. While machine learning models, particularly PINNs, have shown promise in solving DEs, their ability to capture multiple solutions remains underexplored. In this work, we propose a simple and practical approach using PINNs to learn and discover multiple solutions. We first demonstrate that PINNs, when combined with random initialization and deep ensemble method—originally developed for uncertainty quantification—can effectively uncover multiple solutions to nonlinear ordinary and partial DEs. Although training large ensembles of PINNs may appear computationally demanding, this can be done efficiently using vectorization techniques supported by modern deep learning frameworks, allowing many networks to be trained simultaneously. Our approach highlights the critical role of initialization in shaping solution diversity, addressing an often-overlooked aspect of machine learning for scientific computing. Furthermore, we propose utilizing PINN-generated solutions as initial conditions or initial guesses for conventional numerical solvers to enhance accuracy and efficiency in capturing multiple solutions. Extensive numerical experiments, including the Allen–Cahn equation and cavity flow, where our approach successfully identifies both stable and unstable solutions, validate the effectiveness of our method. These findings establish a general and efficient framework for addressing solution multiplicity in nonlinear DEs.

97 MATHEMATICS AND COMPUTING↗

Multi‐Model Ensembles in Ecosystem Modeling: Challenges and Best Practices for Decision‐Making

Ecosystem models are increasingly central to the decision-making for environmental policy, conservation planning, and climate-related investments. Yet, the growing reliance on Multi-Model Ensembles (MMEs) of ecosystem models by practitioners and policymakers, sometimes under tight timelines and imperfect information, has frequently outpaced the scientific rigor required to ensure ensemble reliability. Here, MMEs refer to approaches that combine targeted predictions from multiple models with the expectation of improving robustness and quantifying predictive uncertainty. Poorly designed MMEs may create a false sense of confidence and lead to suboptimal policy and market decisions. This perspective argues that robust decision-making-relevant MMEs must be grounded on two pillars: (1) rigorous Model Intercomparison Projects (MIPs), which identify inter-model agreement and disagreement, characterize model uncertainties, and evaluate robustness with observationally based benchmarks—MIPs' diagnostic evaluation is so critical that it must be needed to drive MME's decision in model selection and weighting, especially when only a limited number of models available; and (2) co-design by both stakeholders and scientists to ensure that scenarios, metrics and uncertainty requirements provide decision-relevant information. Building upon the past success and lessons from the existing MIPs-MMEs efforts (e.g., climate/Earth system/crop), we derived the theoretical basis for MMEs, addressed their specific challenges in ecosystem modeling, and highlighted proper consideration of model numbers and diversity, risk of model inter-dependence, effective calibration of model parameters, possible overdue of some ecosystem model development, critical roles of open benchmark data across a wide range of conditions, and suggested use of Artificial Intelligence to support MIPs-MMEs. We highlighted the under-recognized opportunity for MIPs and MMEs to drive scientific progress and innovation through identifying better performing models, systematic benchmarking, feedback loops, and targeted model improvement. By following actionable best practice guidelines, MMEs can evolve from ad hoc aggregation of models into a trusted backbone of environmental policy and decision-making.

ecosystem modeling↗

Robustness of the Ensemble Score Filter to the Type of Assimilated Observation Networks

Recent advances in data assimilation (DA) have focused on developing more flexible approaches that can better accommodate nonlinearities in models and observations. However, it remains unclear how the performance of these advanced methods depends on the observation network characteristics. In this study, we present initial experiments with the surface quasi‐geostrophic model, in which we compare a recently developed ensemble filter using score‐based diffusion models with the standard Local Ensemble Transform Kalman Filter (LETKF). Our results show that the analysis solutions respond differently to the number, spatial distribution, and nonlinear fraction of assimilated observations. We also find notable changes in the multiscale characteristics of the analysis errors. Given that standard DA techniques will eventually be replaced by more advanced methods, we hope this study sets the ground for future efforts to reassess the value of Earth observing systems in the context of newly emerging algorithms.

97 MATHEMATICS AND COMPUTING↗

Novel PtNi single-atom–nanocluster (SA–NC) ensembles promote Tafel kinetics and ampere-class AEM hydrogen evolution

The development of efficient, durable, and low-PGM electrocatalysts for the hydrogen evolution reaction (HER) in alkaline media is critical for next-generation electrolysis technologies. We report a facile two-step synthesis of highly dispersed PtNi and PtNi-nitride nanoclusters (NCs) (~2.3 nm) with ultralow Pt content (0.5 at.%) anchored on N-doped Vulcan carbon. Structural and compositional characterization via XAS, XPS, HAADF-STEM, HRTEM, and EDS mapping established key structure–activity relationships across varying Pt/Ni ratios and pyrolysis temperatures. The Pt0.5Ni0.5/C-750 catalyst, an ensemble of PtNi M-N-C type single-atom (SA) moieties with neighboring PtNi nanoclusters (NC), exhibited superior HER performance in alkaline media, achieving overpotentials of 30, 115, and 210 mV at 10, 100, and 500 mA cm−2, respectively. Despite at a lower Pt content, this novel SA–NC ensemble outperformed commercial Pt/C by ~36%. A standardized literature comparison with contemporary Pt- and Ru-doped analogues reveals the as-prepared Pt0.5Ni0.5/C-750 to sit at the apex of Tafel-limited kinetics and low overpotential at 100 mA cm−2. Tafel-limited Tafel slopes in both alkaline and acidic regimes confirm favorable proton recombination kinetics. Mass activities at 200 mV reached 13.8 and 18.84 A mgPt−1 in alkaline and acidic media, respectively. However, excessive nitridation (e.g., at 650 °C) adversely altered Pt electronic structure and HER kinetics. While Ni enhanced alkaline HER, acidic HER favored Ni-free analogues. Pt0.5Ni0.5/C-750 also demonstrated robust temperature responsiveness and 300-h operational stability at high current densities (0.5–1.0 A cm−2) in MEA tests. This work presents a scalable strategy for designing thermally responsive, durable, and compositionally tunable NC catalysts with neighboring SA moieties for alkaline electrolysis.

AEMWE↗

Ensemble cure kinetics network (ECK-Net): A method to derive cure kinetics of thermosetting resin

This paper introduces an Ensemble Cure Kinetics Network (ECK-Net), a neural network (NN)–based framework for modeling the cure kinetics of thermosetting resins within a phenomenological context. ECK-Net replaces traditional analytic models, which require extensive chemical insight and multiple isothermal/non-isothermal experiments, with a data-driven surrogate that maps nonlinear relationships between temperature, degree of cure, and reaction rate from differential scanning calorimetry data. The proposed approach predicts input-dependent kinetic coefficients of a generalized nth-order reaction equation rather than reaction rates directly, enabling a single unified model to represent various epoxy systems without relying on iso-conversional analysis or predefined functional forms. To ensure robustness, multiple independently trained networks under different random initializations are blended through an ensemble strategy, effectively mitigating the stochastic variability inherent to neural networks. The framework is validated using experimental datasets from multiple resin systems, including aerospace-grade materials (Toray 3900-2, Cycom 5320-1, and Hexcel 8552) and a windmill-grade resin (RIMR 035c). The model accurately reproduces the temporal evolution of the degree of cure under manufacturers’ recommended cure cycles across all tested resins systems, yielding Pearson’s correlation coefficients of 0.992, 0.994, 0.993, 0.997, respectively. To demonstrate process-level applicability, the trained network was implemented within the Abaqus environment to simulate out-of-autoclave (OOA) curing process of the CFRP panel composed of Toray T830H-6K/3900-2D prepreg. The simulation results showed excellent agreement with experimental temperature response (maximum peak temperature, simulation: 189.6 °C, experiment: 188.5 °C) and the final degree of cure (simulation: 0.948, experiment: 0.960 ± 0.013), confirming ECK-Net’s capability as a reliable alternative to conventional cure kinetics modeling methods.

Composite curing↗

Ensemble Monte Carlo calculations with five novel moves

We introduce five novel types of Monte Carlo (MC) moves that brings the number of moves of ensemble MC calculations from three to eight. So far such calculations have relied on affine invariant stretch moves that were originally introduced by Christen (2007), walk moves by Goodman and Weare (2010) and quadratic moves by Militzer (2023). Ensemble MC methods have been very popular because they harness information about the fitness landscape from a population of walkers rather than relying on expert knowledge. Here we modified the affine method and employed a simplex of points to set the stretch direction. We adopt the simplex concept to quadratic moves. We also generalize quadratic moves to arbitrary order. Finally, we introduce directed moves that employ the values of the probability density while all other types of moves rely solely on the location of the walkers. We apply all algorithms to the Rosenbrock density in 2 and 20 dimensions and to the ring potential in 12 and 24 dimensions. We evaluate their efficiency by comparing error bars, autocorrelation time, travel time, and the level of cohesion that measures whether any walkers were left behind. Our code is open source.

97 MATHEMATICS AND COMPUTING↗

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↗

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↗