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DOE OSTI2020

Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks

Comorbidities such as anemia or hypertension and physiological factors related to exertion can influence a patient’s hemodynamics and increase the severity of many cardiovascular diseases. Observing and quantifying associations between these factors and hemodynamics can be difficult due to the multitude of co-existing conditions and blood flow parameters in real patient data. Machine learning-driven, physics-based simulations provide a means to understand how potentially correlated conditions may affect a particular patient. Here, we use a combination of machine learning and massively parallel computing to predict the effects of physiological factors on hemodynamics in patients with coarctation of the aorta. We first validated blood flow simulations against in vitro measurements in 3D-printed phantoms representing the patient’s vasculature. We then investigated the effects of varying the degree of stenosis, blood flow rate, and viscosity on two diagnostic metrics – pressure gradient across the stenosis (ΔP) and wall shear stress (WSS) - by performing the largest simulation study to date of coarctation of the aorta (over 70 million compute hours). Using machine learning models trained on data from the simulations and validated on two independent datasets, we developed a framework to identify the minimal training set required to build a predictive model on a per-patient basis. We then used this model to accurately predict ΔP (mean absolute error within 1.18 mmHg) and WSS (mean absolute error within 0.99 Pa) for patients with this disease.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Resolving ECRH deposition broadening due to edge turbulence in DIII-D

Microwave heat pulse propagation experiments have demonstrated a correlation between millimeter-scale turbulence and deposition profile broadening of electron cyclotron (EC) waves on the DIII-D tokamak. In a set of discharges in DIII-D, a variation in edge density fluctuations on the mm-scale is associated with 40%–150% broader deposition profiles, expressed in terms of normalized minor radius, as compared with equilibrium ray tracing. The 1D power profile is determined from transport analysis of the electron temperature response to EC power modulation using perturbative analysis with a square wave power modulation at 20–70 Hz, producing a series of Fourier harmonics that are fit collectively to resolve transport. Fitting an integrated heat flux expressed in the Fourier basis of the modulation to diffusive, convective, and coupled transport terms in a linear model can resolve the broadened EC deposition width from the power perturbation to resolve a broadening in each case. The best fit degree of beam broadening observed scales approximately linearly with the Doppler backscattering measured fluctuation level in the steep gradient region. Quantifying the effect of edge fluctuation broadening on EC current drive power needs of future devices will require 3D full-wave codes that can be validated on the current generation of machines. These DIII-D experiments provide a quantitative measure of fluctuation effects and a dataset to benchmark full-wave simulations that can model and eventually predict nonlinear effects neglected by 1D equilibrium beam and ray tracing.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Characterization of uncertainties in electron-argon collision cross sections

Abstract The predictive capability of a plasma discharge model depends on accurate representations of electron-impact collision cross sections, which determine the corresponding reaction rates and electron transport properties. The values of cross sections can be known only approximately either through experiments or simulations and are thus subject to uncertainties. Quantifying the uncertainties in plasma simulations allows us to assess the reliability of simulations and to provide a basis for interpreting discrepancies between simulations and experiments. For such uncertainty quantification of plasma simulations, it is essential to quantify the uncertainties of the underlying cross sections. Although much effort has been committed to calibrate the cross section values, their uncertainties are not well investigated. We characterize uncertainties in electron-argon atom collision cross sections using a Bayesian framework. Six collision processes—elastic momentum transfer, ionization, and four excitations—are characterized with semi-empirical models, which effectively capture the features important to the macroscopic properties of the plasma. A probability model for the uncertain parameters of these semi-empirical models is developed. Specifically, a Gaussian-process likelihood model is proposed to capture discrepancies among data sets, as well as the model-form inadequacies of the semi-empirical models. Two other likelihood models are compared with the proposed Gaussian-process model, to illustrate the importance of the choice of the likelihood model. The cross section models are calibrated using the electron-beam experiments and ab-inito quantum simulations. The resulting calibrated uncertainties capture well the scattering among the data sets. The calibrated cross section models are further validated against swarm-parameter experiments and zero-dimensional Boltzmann equation simulations of widely used cross section datasets.

Chung, Seung Whan (ORCID:0000000302501549)↗

DOE OSTI2017

A model independent safeguard against background mismodeling for statistical inference

We propose a safeguard procedure for statistical inference that provides universal protection against mismodeling of the background. The method quantifies and incorporates the signal-like residuals of the background model into the likelihood function, using information available in a calibration dataset. This prevents possible false discovery claims that may arise through unknown mismodeling, and corrects the bias in limit setting created by overestimated or underestimated background. We demonstrate how the method removes the bias created by an incomplete background model using three realistic case studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Comparison of three DWM-based wake models at above-rated wind speeds

In this study we investigate three mid-fidelity wind turbine wake models based on the dynamic wake meandering (DWM) model principle, and compare their performance with a reference dataset, produced with large-eddy simulations using the actuator line model. The models are compared with respect to flow field, power, and loads on a row of four 5MW reference turbines experiencing above-rated wind conditions. In general, the DWM models show fairly good agreement with large-eddy simulation for the time-averaged flow fields, blade forces and power, with increasing differences along the turbine row. Also when comparing fatigue loads of blade root moments, the differences between the models increase further into the row, with deviations up to 25 % of the reference case. However, while the development in blade root moment fatigue along the turbine row is predominantly driven by the energy content at the frequency corresponding to the turbine's rotational period (1 P ) for the DWM models, the large-eddy simulation results suggest that the key drivers for the blade root and tower loads are the increase in meandering and energy at higher frequencies (> 1 P ) deeper into the turbine row. For the tower loads, the DWM models highly underestimate the fatigue for the waked turbines. From these results, we suggest priorities for future model developments so that robust model implementations can be used in wind farm design and operation.

17 WIND ENERGY↗

DOE OSTI2017

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyl transfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Foundation model framework for all tasks involving jet physics

Foundation models use large datasets to build an effective representation of data that can be deployed on diverse downstream tasks. Previous research developed the omnilearn foundation model for jet physics, using unique properties of particle physics, and showed that it could significantly advance discovery potential across collider experiments. This paper introduces a major upgrade, resulting in the omnilearned framework. This framework has three new elements: (1) updates to the model architecture and training, (2) using over 1 × 10 9 jets used for training, and (3) providing well-documented software for accessing all datasets and models. We demonstrate omnilearned with three representative tasks: top-quark jet tagging with the community delphes-based benchmark dataset, b tagging with ATLAS full simulation, and anomaly detection with CMS experimental data. In each case, omnilearned is the state of the art, further expanding the discovery potential of past, current, and future collider experiments.

Bhimji, Wahid [Lawrence Berkeley National Laborato↗

DOE OSTI2025

Method to simultaneously facilitate all jet physics tasks

Machine learning has become an essential tool in jet physics. Due to their complex, high-dimensional nature, jets can be explored holistically by neural networks in ways that are not possible manually. However, innovations in all areas of jet physics are proceeding in parallel. We show that specially constructed machine learning models trained for a specific jet classification task can improve the accuracy, precision, or speed of all other jet physics tasks. This is demonstrated by training on a particular multiclass generation and classification task and then using the learned representation for different generation and classification tasks, for datasets with a different (full) detector simulation, for jets from a different collision system ($pp$ versus $ep$), for generative models, for likelihood ratio estimation, and for anomaly detection. We consider our omnilearn approach thus as a jet-physics foundation model. It is made publicly available for use in any area where state-of-the-art precision is required for analyses involving jets and their substructure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction

Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Exploring Memory Hierarchy to Improve Scientific Data Read Performance, In: 2015 IEEE International Conference on Cluster Computing

Improving read performance is one of the major challenges with speeding up scientific data analytic applications. Utilizing the memory hierarchy is one major line of researches to address the read performance bottleneck. Related methods usually combine solide-state-drives(SSDs) with dynamic random-access memory(DRAM) and/or parallel file system(PFS) to mitigate the speed and space gap between DRAM and PFS. However, these methods are unable to handle key performance issues plaguing SSDs, namely read contention that may cause up to 50% performance reduction. In this paper, we propose a framework that exploits the memory hierarchy resource to address the read contention issues involved with SSDs. The framework employs a general purpose online read algorithm that able to detect and utilize memory hierarchy resource to relieve the problem. To maintain a near optimal operating environment for SSDs, the framework is able to orchastrate data chunks across different memory layers to facilitate the read algorithm. Compared to existing tools, our framework achieves up to 50% read performance improvement when tested on datasets from real-world scientific simulations.

Computer Science↗

DOE OSTI2022

Using Image Processing Techniques to Identify and Quantify Spatiotemporal Carbon Cycle Extremes

Rising atmospheric carbon dioxide due to human activities through fossil fuel emissions and land use changes have increased climate extremes such as heat waves and droughts that have led to and are expected to increase the occurrence of carbon cycle extremes. Carbon cycle extremes represent large anomalies in the carbon cycle that are associated with gains or losses in carbon uptake. Carbon cycle extremes could be continuous in space and time and cross political boundaries. Here, we present a methodology to identify large spatiotemporal extremes (STEs) in the terrestrial carbon cycle using image processing tools for feature detection. We characterized the STE events based on neighborhood structures that are three-dimensional adjacency matrices for the detection of spatiotemporal manifolds of carbon cycle extremes. We found that the area affected and carbon loss during negative carbon cycle extremes were consistent with continuous neighborhood structures. In the gross primary production data we used, 100 carbon cycle STEs accounted for more than 75% of all the negative carbon cycle extremes. This paper presents a comparative analysis of the magnitude of carbon cycle STEs and attribution of those STEs to climate drivers as a function of neighborhood structures for two observational datasets and an Earth system model simulation.

Sharma, Bharat↗

DOE OSTI2021

A Hybrid System for Learning Classical Data in Quantum States

Deep neural network-powered artificial intelligence has rapidly changed our daily life with various applications. However, as one of the essential steps of deep neural networks, training a heavily-weighted network requires a tremendous amount of computing resources. Especially in the post Moore’s Law era, the limit of semiconductor fabrication technology has restricted the development of learning algorithms to cope with the increasing high intensity training data. Meanwhile, quantum computing has exhibited its significant potential in terms of speeding up the traditionally compute-intensive workloads. For example, Google illustrates quantum supremacy by completing a sampling calculation task in 200 seconds, which is otherwise impracticable on the world’s largest supercomputers. To this end, quantum-based learning becomes an area of interest, with the promising of a quantum speedup. In this paper, we propose GenQu, a hybrid and general-purpose quantum framework for learning classical data through quantum states. We evaluate GenQu with real datasets and conduct experiments on both simulations and real quantum computer IBM-Q. Our evaluation demonstrates that, comparing with classical solutions, the proposed models running on GenQu framework achieve similar accuracy with a much smaller number of qubits, while significantly reducing the parameter size by up to 95.86% and converging speedup by 66.67% faster.

Stein, Samuel A.↗

DOE OSTI2014

An algorithm to estimate the object support in truncated images

Purpose: Truncation artifacts in CT occur if the object to be imaged extends past the scanner field of view (SFOV). These artifacts impede diagnosis and could possibly introduce errors in dose plans for radiation therapy. Several approaches exist for correcting truncation artifacts, but existing correction algorithms do not accurately recover the skin line (or support) of the patient, which is important in some dose planning methods. The purpose of this paper was to develop an iterative algorithm that recovers the support of the object. Methods: The authors assume that the truncated portion of the image is made up of soft tissue of uniform CT number and attempt to find a shape consistent with the measured data. Each known measurement in the sinogram is interpreted as an estimate of missing mass along a line. An initial estimate of the object support is generated by thresholding a reconstruction made using a previous truncation artifact correction algorithm (e.g., water cylinder extrapolation). This object support is iteratively deformed to reduce the inconsistency with the measured data. The missing data are estimated using this object support to complete the dataset. The method was tested on simulated and experimentally truncated CT data. Results: The proposed algorithm produces a better defined skin line than water cylinder extrapolation. On the experimental data, the RMS error of the skin line is reduced by about 60%. For moderately truncated images, some soft tissue contrast is retained near the SFOV. As the extent of truncation increases, the soft tissue contrast outside the SFOV becomes unusable although the skin line remains clearly defined, and in reformatted images it varies smoothly from slice to slice as expected. Conclusions: The support recovery algorithm provides a more accurate estimate of the patient outline than thresholded, basic water cylinder extrapolation, and may be preferred in some radiation therapy applications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

TU-C-17A-08: Improving IMRT Planning and Reducing Inter-Planner Variability Using the Stochastic Frontier Method: Validation Based On Clinical and Simulated Data

Purpose: Intensity modulated radiation therapy always requires compromises between PTV coverage and organs at risk (OAR) sparing. We previously developed metrics that correlate doses to OAR to specific patients’ morphology using stochastic frontier analysis (SFA). Here, we aim to examine the validity of this approach using a large set of realistically simulated dosimetric and geometric data. Methods: SFA describes a set of treatment plans as an asymmetric distribution with respect to a frontier defining optimal plans. Eighty head and neck IMRT plans were used to establish a metric predicting the mean dose to parotids as a function of simple geometric parameters. A database of 140 parotids was used as a basis distribution to simulate physically plausible data of geometry and dose. Distributions comprising between 20 and 5000 were simulated and the SFA was applied to obtain new frontiers, which were compared to the original frontier. Results: It was possible to simulate distributions consistent with the original dataset. Below 160 organs, the SFA could not always describe distributions as asymmetric: a few cases showed a Gaussian or half-Gaussian distribution. In order to converge to a stable solution, the number of organs in a distribution must ideally be above 100, but in many cases stable parameters could be achieved with as low as 60 samples of organ data. Mean RMS value of the error of new frontiers was significantly reduced when additional organs are used. Conclusion: The number of organs in a distribution showed to have an impact on the effectiveness of the model. It is always possible to obtain a frontier, but if the number of organs in the distribution is small (< 160), it may not represent de lowest dose achievable. These results will be used to determine number of cases necessary to adapt the model to other organs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Iterative metal artifact reduction for x-ray computed tomography using unmatched projector/backprojector pairs

Purpose: Metal artifact reduction (MAR) is a major problem and a challenging issue in x-ray computed tomography (CT) examinations. Iterative reconstruction from sinograms unaffected by metals shows promising potential in detail recovery. This reconstruction has been the subject of much research in recent years. However, conventional iterative reconstruction methods easily introduce new artifacts around metal implants because of incomplete data reconstruction and inconsistencies in practical data acquisition. Hence, this work aims at developing a method to suppress newly introduced artifacts and improve the image quality around metal implants for the iterative MAR scheme. Methods: The proposed method consists of two steps based on the general iterative MAR framework. An uncorrected image is initially reconstructed, and the corresponding metal trace is obtained. The iterative reconstruction method is then used to reconstruct images from the unaffected sinogram. In the reconstruction step of this work, an iterative strategy utilizing unmatched projector/backprojector pairs is used. A ramp filter is introduced into the back-projection procedure to restrain the inconsistency components in low frequencies and generate more reliable images of the regions around metals. Furthermore, a constrained total variation (TV) minimization model is also incorporated to enhance efficiency. The proposed strategy is implemented based on an iterative FBP and an alternating direction minimization (ADM) scheme, respectively. The developed algorithms are referred to as “iFBP-TV” and “TV-FADM,” respectively. Two projection-completion-based MAR methods and three iterative MAR methods are performed simultaneously for comparison. Results: The proposed method performs reasonably on both simulation and real CT-scanned datasets. This approach could reduce streak metal artifacts effectively and avoid the mentioned effects in the vicinity of the metals. The improvements are evaluated by inspecting regions of interest and by comparing the root-mean-square errors, normalized mean absolute distance, and universal quality index metrics of the images. Both iFBP-TV and TV-FADM methods outperform other counterparts in all cases. Unlike the conventional iterative methods, the proposed strategy utilizing unmatched projector/backprojector pairs shows excellent performance in detail preservation and prevention of the introduction of new artifacts. Conclusions: Qualitative and quantitative evaluations of experimental results indicate that the developed method outperforms classical MAR algorithms in suppressing streak artifacts and preserving the edge structural information of the object. In particular, structures lying close to metals can be gradually recovered because of the reduction of artifacts caused by inconsistency effects.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Designing an Optimal Sensor Network via Minimizing Information Loss

Optimal experimental design is a classic topic in statistics, with many well-studied problems, applications, and solutions. The design problem we study is the placement of sensors to monitor spatiotemporal processes, explicitly accounting for the temporal dimension in our modeling and optimization. We observe that recent advancements in computational sciences often yield large datasets based on physics-based simulations, which are rarely leveraged in experimental design. We introduce a novel model-based sensor placement criterion, along with a highly-efficient optimization algorithm, which integrates physics-based simulations and Bayesian experimental design principles to identify sensor networks that “minimize information loss” from simulated data. Our technique relies on sparse variational inference and (separable) Gauss-Markov priors, and thus may adapt many techniques from Bayesian experimental design. We validate our method through a case study monitoring air temperature in Phoenix, Arizona, using state-of-the-art physics-based simulations. Our results show our framework to be superior to random or quasi-random sampling, particularly with a limited number of sensors. We conclude by discussing practical considerations and implications of our framework, including more complex modeling tools and real-world deployments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Active-wake mixing in atmospheric boundary layers with one-turbine arrays

This dataset includes results of high fidelity simulations of a single, offshore wind turbine under a variety of atmospheric conditions. Of primary interest is the turbine performance and wake characteristics when different turbine control strategies are applied, including when wake steering or active wake control are used. The simulations were performed with the LES code AMR-Wind (https://github.com/Exawind/amr-wind/), coupled with OpenFAST (https://github.com/OpenFAST/openfast) and the ROSCO open-source turbine controller (https://github.com/NREL/ROSCO). The turbine used in the simulations is the IEA 15MW reference turbine model.

17 WIND ENERGY↗

DOE OSTI2026

Evaluating multi-slice ptychography tomography for X-ray imaging

X-ray ptychography typically relies on single-slice reconstruction approaches that assume minimal beam propagation through the specimen. However, this approximation breaks down for thick samples or when using high numerical aperture optics, leading to reconstruction artifacts due to multiple scattering. Multi-slice ptychographic tomography (MSPT) addresses this limitation by explicitly modeling beam propagation through the specimen while reducing angular sampling requirements for tomography, but its performance depends critically on reconstruction parameters and experimental conditions. Here, we systematically evaluate MSPT using numerical simulations and experimental X-ray datasets to understand how factors such as object thickness, optical parameters, and initialization strategies affect reconstruction accuracy. We demonstrate that informed object initialization significantly improves depth resolution and enables accurate projection extension, reducing the angular sampling requirements for tomographic reconstruction. Experimental demonstration confirms that MSPT produces reconstructions with reduced artifacts, establishing it as a robust approach for nanoscale imaging at modern synchrotron facilities.

Luktuke, Amey [Argonne National Laboratory (ANL), ↗