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DOE OSTI2021

Changes in Annual Extremes of Daily Temperature and Precipitation in CMIP6 Models

This study presents an analysis of daily temperature and precipitation extremes with return periods ranging from 2 to 50 years in phase 6 of the Coupled Model Intercomparison Project (CMIP6) multimodel ensemble of simulations. Judged by similarity with reanalyses, the new-generation models simulate the present-day temperature and precipitation extremes reasonably well. In line with previous CMIP simulations, the new simulations continue to project a large-scale picture of more frequent and more intense hot temperature extremes and precipitation extremes and vanishing cold extremes under continued global warming. Changes in temperature extremes outpace changes in global annual mean surface air temperature (GSAT) over most landmasses, while changes in precipitation extremes follow changes in GSAT globally at roughly the Clausius–Clapeyron rate of ~7% °C –1 . Changes in temperature and precipitation extremes normalized with respect to GSAT do not depend strongly on the choice of forcing scenario or model climate sensitivity, and do not vary strongly over time, but with notable regional variations. Over the majority of land regions, the projected intensity increases and relative frequency increases tend to be larger for more extreme hot temperature and precipitation events than for weaker events. To obtain robust estimates of these changes at local scales, large initial-condition ensemble simulations are needed. Appropriate spatial pooling of data from neighboring grid cells within individual simulations can, to some extent, reduce the needed ensemble size.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

A Diffusion‐Based Uncertainty Quantification Method to Advance E3SM Land Model Calibration

Abstract Calibrating land surface models and accurately quantifying their uncertainty are crucial for improving the reliability of simulations of complex environmental processes. This, in turn, advances our predictive understanding of ecosystems and supports climate‐resilient decision‐making. Traditional calibration methods, however, face challenges of high computational costs and difficulties in accurately quantifying parameter uncertainties. To address these issues, we develop a diffusion‐based uncertainty quantification (DBUQ) method. Unlike conventional generative diffusion methods, which are computationally expensive and memory‐intensive, DBUQ innovates by formulating a parameterized generative model and approximates this model through supervised learning, which enables quick generation of parameter posterior samples to quantify its uncertainty. DBUQ is effective, efficient, and general‐purpose, making it suitable for site‐specific ecosystem model calibration and broadly applicable for parameter uncertainty quantification across various earth system models. In this study, we applied DBUQ to calibrate the Energy Exascale Earth System Model land model at the Missouri Ozark AmeriFlux forest site. Results indicated that DBUQ produced accurate parameter posterior distributions similar to those from Markov Chain Monte Carlo sampling but with 30 times less computing time. This significant improvement in efficiency suggests that DBUQ can enable rapid, site‐level model calibration at a global scale, enhancing our predictive understanding of climate impacts on terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Training a Quantum Annealing Based Restricted Boltzmann Machine on Cybersecurity Data

A restricted Boltzmann machine (RBM) is a generative model that could be used in effectively balancing a cybersecurity dataset because the synthetic data a RBM generates follows the probability distribution of the training data. RBM training can be performed using contrastive divergence (CD) and quantum annealing (QA). QA-based RBM training is fundamentally different from CD and requires samples from a quantum computer. We present a real-world application that uses a quantum computer. Specifically, we train a RBM using QA for cybersecurity applications. The D-Wave 2000Q has been used to implement QA. RBMs are trained on the ISCX data, which is a benchmark dataset for cybersecurity. For comparison, RBMs are also trained using CD. CD is a commonly used method for RBM training. Our analysis of the ISCX data shows that the dataset is imbalanced. We present two different schemes to balance the training dataset before feeding it to a classifier. The first scheme is based on the undersampling of benign instances. The imbalanced training dataset is divided into five sub-datasets that are trained separately. A majority voting is then performed to get the result. Our results show the majority vote increases the classification accuracy up from 90.24% to 95.68%, in the case of CD. For the case of QA, the classification accuracy increases from 74.14% to 80.04%. In the second scheme, a RBM is used to generate synthetic data to balance the training dataset. We show that both QA and CD-trained RBM can be used to generate useful synthetic data. Balanced training data is used to evaluate several classifiers. Among the classifiers investigated, K-Nearest Neighbor (KNN) and Neural Network (NN) perform better than other classifiers. They both show an accuracy of 93%. Our results show a proof-of-concept that a QA-based RBM can be trained on a 64-bit binary dataset. The illustrative example suggests the possibility to migrate many practical classification problems to QA-based techniques. Further, we show that synthetic data generated from a RBM can be used to balance the original dataset.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Explicit physics-informed neural networks for nonlinear closure: The case of transport in tissues

In upscaling methods, closures for nonlinear problems present a well-known challenge. While a number of theoretical methods have been proposed for handling such closures, nonlinearities still remain a significant obstacle for many problems. In this work, we use a combination of formal upscaling and data-driven machine learning for explicitly closing a nonlinear transport and reaction process in multiscale tissues. The classical effectiveness factor model is used to formulate the macroscale reaction kinetics. We train a multilayer perceptron network using training data generated by direct numerical simulations over microscale examples. Once trained, the network is used in an algorithm for numerically solving the upscaled (coarse-grained) differential equation describing mass transport and reaction in two example tissues. The network is described as being explicit in the sense that the network is trained using macroscale concentrations and gradients of concentration as components of the feature space rather than incorporating them as part of a constraint in the optimization process. Network training and solutions to the macroscale transport equations were computed for two different tissues. The two tissue types (brain and liver) exhibit markedly different geometrical complexity and spatial scale (cell size and sample size). The upscaled solutions for the average concentration are compared with numerical solutions derived from the microscale concentration fields by a posteriori averaging. There are three outcomes of this work of particular note. 1) Our overall approach results in an upscaled nonlinear PDE. The PDE is closed using a neural network, and our approach results in the definition of the classical effectiveness factor for effecting closure. 2) We identify particular source terms for the closure problem that are important for representing the structure of the closure. These source terms involve macroscale concentrations and their gradients. We adopt these source terms to use as explicit features in the learning algorithm. We find the trained networks that include the macroscale source terms generate models that are able to predict the correction factor with increased fidelity over those that do not. 3) We find that the trained network exhibits good generalizability, and it is able to predict the effectiveness factor with high fidelity for realistically-structured tissues despite the significantly different scale and geometrical complexity of the two example tissue types. This latter result emphasizes our purposeful connection between conventional averaging methods with the use of machine learning for closure; this contrasts with some machine learning methods for upscaling where the exact form of the macroscale equation remains unknown.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

pyflowline: a mesh-independent river network generator for hydrologic models

River networks are crucial in hydrologic and Earth system models. Accurately representing river networks in spatially distributed hydrologic models requires considering the model's spatial discretization and computational mesh. However, current methods of generating river networks for hydrologic models do not typically support unstructured meshes. Unstructured meshes offer numerous advantages over traditional, structured meshes. To overcome this limitation, we developed PyFlowline, a Python package that generates mesh-independent river networks. With PyFlowline, hydrologic modelers can generate conceptual river networks and their topological relationships for both structured and unstructured meshes.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Spatiotemporal forecasting of the edge localized modes in tokamak plasmas using neural networks

Artificial intelligence techniques have been increasingly adopted by the plasma and fusion science to address problems like plasma reconstruction, surrogate modeling, and tokamak/stellarator optimization. A key focus in sustained fusion research is the prediction and mitigation of edge-localized-modes (ELMs), instabilities that occur in short, periodic bursts and can cause erosion to the tokamak vessel wall. Recent research has demonstrated the power of neural networks in approximating continuous functions. In this work, we build spatiotemporal forecasting models that can predict the onset of ELMs and their evolution at early stages. We leverage recent advances in generative modeling, sequence-to-sequence modeling, and Fourier neural operators to propose architectures and training strategies that can learn to forecast short to long term dynamics of the noisy signals due to ELMs. We benchmark the developed model against a state-of-the-art foundation model using the beam emission spectroscopy (BES) data that captures the plasma fluctuations due to ELMs over a 8 x 8 spatial grid. Our models demonstrate high accuracy, outperforming the baselines, in predicting the evolution of BES signals during ELM events. Furthermore, the developed models exhibit high accuracy in predicting the rapid rise and relaxation of the signals due to ELMs within 30–80 µs.

edge localized modes↗

DOE OSTI2025

PNNL-CompBio/3D_Scaffold

A domain-aware generative framework that takes 3D coordinates of the molecule and scaffold as an input and generates 3D coordinates of novel therapeutic candidates as an output while preserving the desired scaffolds. We show that our model generates predominantly valid, unique, novel, and experimentally synthesizable molecules that have drug-like properties similar to the molecules in the training set

Kumar, Neeraj [Pacific Northwest National Laborato↗

DOE OSTI2021

BETO 2021 Peer Review - WBS 4.1.2.32: Bioeconomy Scenario Analysis

The Bioeconomy Scenario Analysis project uses systems thinking and analysis to assess current and/or prospective techno-economics, research and development, deployment strategies, policy, and market conditions and their impact on the potential development trajectories of the bioenergy industry over time. Results from this project include identification of opportunities and constraints to industrial development, quantification of multiple metrics (energy, economic, environmental) and informing researchers, decision makers, and industry of the steps needed for a sustainable, nationwide biofuels industry. Analyses from this project enable the creation of a bioenergy industry by (1) inciting policy-makers to explore scenarios for nationwide biofuels production, identifying policy actions consistent with pathways for growth; (2) improving industry’s understanding of industry growth potential under different technology and investment conditions, better targeting their development efforts; and (3) providing universities and other interested stakeholders with tools and analyses that can be adapted to meet research and teaching objectives, connecting students with careers that build the industry. One of the many modeling tools used in this project, the Biomass Scenario Model (BSM) is a publicly-available, unique, validated, state-of-the-art, award-winning, fourth-generation model of the domestic biofuels supply chain which explicitly focuses on how and under what conditions biofuel technologies might be deployed to contribute to the U.S. transportation energy sector. We use models like the BSM to examine the implications of policies and incentives as well as their potential side-effects. The BSM uses a system-dynamics simulation to model dynamic interactions and transitions across the supply chain; it tracks the deployment of biofuels given industrial learning and the reaction of the investment community in the context of land availability, projected oil markets, consumer demand for biofuels, and government policies over time. Under expected market conditions, analyses using the BSM suggest that the biofuels industry may require significant external actions in the early years to thrive. Interventions that accelerate the industrial learning process (e.g. operation of pre-commercial and commercial facilities) have been identified as having strong influence in starting the growth of a commercial biofuel industry. Policies which are coordinated across the whole supply chain in BSM foster the growth of the biofuels industry and production of tens of billions of gallons of biofuels may occur under sufficiently favorable conditions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Bioeconomy Scenario Analysis

The Bioeconomy Scenario Analysis (BSA) project uses systems thinking and analysis to assess how techno economics, research and development, deployment strategies, policy, and market conditions affect the potential development trajectories of the developing bioenergy industry. This project informs researchers, decision makers, and industry by identifying opportunities for and constraints to industrial development and quantifying important industry metrics (e.g., energy, economic, environmental) towards a sustainable domestic bioenergy system. One of the tools used in this project, the Bioenergy Scenario Model (BSM) is a publicly-available, unique, validated, state-of-the-art, award-winning, fourth-generation model of the domestic biofuels supply chain which explicitly focuses on how and under what conditions biofuel technologies might be deployed to contribute to the U.S. transportation energy sector. Analysis products from this effort enable the development of the bioenergy industry by (1) encouraging policy-makers to explore multiple levers simulating outside impacts on biofuels production, identifying policy actions; (2) improving industry's understanding of growth potential under different market conditions, better targeting their development efforts; and (3) providing universities and other interested stakeholders with analysis tools and analyses that can be adapted to meet research and teaching objectives, thus connecting students with careers that build the industry.

bioenergy↗

DOE OSTI2026

LeWRON: Learning ElectroWeak phase tRansitiON with agentic architecture

An agent to analyze electroweak phase transition. LeWRON turns a BSM model description or a reproduction target into a structured run: symbolic setup, effective-potential artifacts, finite-temperature machinery, generated model code, a scientific report, and an interactive exploration session. It keeps both machine-readable artifacts and human-readable notes, so a run can be resumed, audited, revised, and shared.

Wang, Isaac [Fermi National Accelerator Laboratory↗

DOE OSTI2024

Regional-scale fault-to-structure earthquake simulations with the EQSIM framework: Workflow maturation and computational performance on GPU-accelerated exascale platforms

Continuous advancements in scientific and engineering understanding of earthquake phenomena, combined with the associated development of representative physics-based models, is providing a foundation for high-performance, fault-to-structure earthquake simulations. However, regional-scale applications of high-performance models have been challenged by the computational requirements at the resolutions required for engineering risk assessments. The EarthQuake SIMulation (EQSIM) framework, a software application development under the US Department of Energy (DOE) Exascale Computing Project, is focused on overcoming the existing computational barriers and enabling routine regional-scale simulations at resolutions relevant to a breadth of engineered systems. This multidisciplinary software development—drawing upon expertise in geophysics, engineering, applied math and computer science—is preparing the advanced computational workflow necessary to fully exploit the DOE’s exaflop computer platforms coming online in the 2023 to 2024 timeframe. Achievement of the computational performance required for high-resolution regional models containing upward of hundreds of billions to trillions of model grid points requires numerical efficiency in every phase of a regional simulation. This includes run time start-up and regional model generation, effective distribution of the computational workload across thousands of computer nodes, efficient coupling of regional geophysics and local engineering models, and application-tailored highly efficient transfer, storage, and interrogation of very large volumes of simulation data. This article summarizes the most recent advancements and refinements incorporated in the workflow design for the EQSIM integrated fault-to-structure framework, which are based on extensive numerical testing across multiple graphics processing unit (GPU)-accelerated platforms, and demonstrates the computational performance achieved on the world’s first exaflop computer platform through representative regional-scale earthquake simulations for the San Francisco Bay Area in California, USA.

58 GEOSCIENCES↗

DOE OSTI2024

Investigating a Potential Hafnium Bias in SCALE [Slides]

Previous work has examined the evidence for a gadolinium bias within SCALE. This work extends the previous work to include benchmark models with hafnium experiments from the ICSBEP Handbook. VALID contains only one experiment with hafnium: MIX-COMP-THERM-008. Newly generated models provide an opportunity to assess the potential presence of a hafnium bias.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Scalable Truck Charging Demand Simulation for Cost-Optimized Infrastructure Planning

This project developed a scalable, high-resolution model to simulate medium- and heavy-duty (MHD) electric truck charging demand and assess its impact on grid infrastructure. Using generative modeling, simulation, and cost optimization, the project delivered an end-to-end software pipeline and a library of 96 real-world scenarios for the Dallas–Houston megaregion. We demonstrated a modular architecture for transportation and grid modeling, implemented cost-optimized infrastructure planning methods, and quantified grid capital, operational, and environmental costs across a wide range of truck electrification scenarios. The results have been adopted by major utility stakeholders and contributed to regional planning efforts.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Accurate parameterization of the kinetic energy functional for calculations using exact-exchange

In this report, electronic structure calculations based on Kohn-Sham density functional theory (KSDFT) that incorporate exact exchange or hybrid functionals are associated with large computational expense, a consequence of the inherent cubic scaling bottleneck and large associated prefactor, which limits the length and time scales that can be accessed. Though orbital-free density functional theory (OFDFT) calculations scale linearly with system size and are associated with significantly smaller prefactor, they are limited by the absence of accurate density-dependent kinetic energy functionals. Therefore, the development of accurate density-dependent kinetic energy functionals is important for OFDFT calculations of large realistic systems. To this end, we propose a method to train kinetic energy functional models at the exact-exchange level of theory by using a dictionary of physically relevant terms that have been proposed in the literature in conjunction with linear or nonlinear regression methods to obtain the fitting coefficients. For our dictionary, we use gradient expansion of the kinetic energy, nonlocal models proposed in the literature and their nonlinear combinations, such as a model that incorporates spatial correlations between higher order derivatives of electron density at two points. The predictive capabilities of these models are assessed by using a variety of model one-dimensional systems that exhibit diverse bonding characteristics, such as a chain of eight hydrogens, LiF, LiH, C 4 H 2 , C 4 N 2 and C 3 O 2 . We show that by using data from model one-dimensional KSDFT calculations performed using the exact-exchange functional for only a few neutral structures, it is possible to generate models with high accuracy for charged systems as well as electron and kinetic energy densities during self-consistent field iterations. In addition, we show that it possible to learn both the orbital dependent terms, i.e., the kinetic energy and the exact-exchange energy, and models that incorporate additional nonlinearities in spatial correlations, such as a quadratic model, are needed to capture subtle features of the kinetic energy density that are present in exact-exchange-based KSDFT calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

A new Monte Carlo generator for BSM physics in B → K*ℓ+ℓ− decays with an application to lepton non-universality in angular distributions

Abstract Within the widely used EvtGen framework, we have added a new event generator model forB → K * ℓ + ℓ − with improved standard model (SM) decay amplitudes and possible BSM physics contributions, which are implemented in the operator product expansion in terms of Wilson coefficients. This event generator can then be used to estimate the statistical sensitivity of a simulated experiment to the most general BSM signal resulting from dimension-six operators. We describe the advantages and potential of the newly developed ‘Sibidanov Physics Generator’ in improving the experimental sensitivity of searches for lepton non-universal BSM physics and clarifying signatures. The new generator can properly simulate BSM scenarios, interference between SM and BSM amplitudes, and correlations between different BSM observables as well as acceptance bias. We show that exploiting such correlations substantially improves experimental sensitivity. As a demonstration of the utility of the MC generator, we examine the prospects for improved measurements of lepton non-universality in angular distributions forB→K * ℓ + ℓ − decays from the expected 50 ab −1 data set of the Belle II experiment, using a four-dimensional unbinned maximum likelihood fit. We describe promising experimental signatures and correlations between observables. The use of lepton-universality violating ∆-observables significantly reduces uncertainties in the SM expectations due to QCD and resonance effects and is ideally suited for Belle II with the large data sets expected in the next decade. Thanks to the clean experimental environment of ane + e − machine, Belle II should be able to probe BSM physics in the Wilson coefficientsC 7 and$$ {C}_7^{\prime } $$ C 7 ′ , which appear at lowq 2 in the di-electron channel.

Physics↗

DOE OSTI2021

Observability Analysis of a Power System Stochastic Dynamic Model Using a Derivative-Free Approach

Serving as a prerequisite to power system dynamic state estimation, the observability analysis of a power system dynamic model has recently attracted the attention of many power engineers. However, because this model is typically nonlinear and large-scale, the analysis of its observability is a challenge to the traditional derivative-based methods. Indeed, the linear-approximation-based approach may provide unreliable results while the nonlinear-technique-based approach inevitably faces extremely complicated derivations. Furthermore, because power systems are intrinsically stochastic, the traditional deterministic approaches may lead to inaccurate observability analyses. In this work, facing these challenges, we propose a novel polynomial-chaos-based derivative-free observability analysis approach that not only is free of any linear approximations, but also accounts for the stochasticity of the dynamic model while bringing a low implementation complexity. Furthermore, this approach enables us to quantify the degree of observability of a stochastic model, what conventional deterministic methods cannot do. The excellent performance of the proposed method has been demonstrated by performing extensive simulations using a synchronous generator model with IEEE-DC1A exciter and the TGOV1 turbine governor.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy

Accurately simulating the linear and nonlinear electronic spectra of condensed phase systems and accounting for all physical phenomena contributing to spectral line shapes presents a significant challenge. Vibronic transitions can be captured through a harmonic model generated from the normal modes of a chromophore, but it is challenging to also include the effects of specific chromophore–environment interactions within such a model. We work to overcome this limitation by combining approaches to account for both explicit environment interactions and vibronic couplings for simulating both linear and nonlinear optical spectra. We present and show results for three approaches of varying computational cost for combining ensemble sampling of chromophore–environment configurations with Franck–Condon line shapes for simulating linear spectra. We present two analogous approaches for nonlinear spectra. Simulated absorption spectra and two-dimensional electronic spectra (2DES) are presented for the Nile red chromophore in different solvent environments. Furthermore, employing an average Franck–Condon or 2DES line shape appears to be a promising method for simulating linear and nonlinear spectroscopy for a chromophore in the condensed phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗