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DOE OSTI2024

Machine learning approaches for integrating multi-omics data to expand microbiome annotation

Preliminary: This final report corresponds to a grant (DE-SC0021216) that was awarded to the University of Montana. Mid-way through the grant period, I relocated from the University of Montana to the University of Arizona. The grant was ended at University of Montana in late 2022, with all efforts concluding on 08/26/22; the remaining funds supporting the project were relinquished by University of Montana, and were later awarded to University of Arizona under a new grant, with start date 04/01/23. This report focuses on results of research efforts at UMontana through 08/26/22. Results: We made progress in each of the three aims of the proposal. We released software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes. We made substantial progress in developing software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we made notable progress in developing AI methods (specifically: a neural embedding model) for identifying similarities between protein sequences based on amino-wise latent vectors. These efforts were supplemented by development of methods for protein modeling in support of predicting protein-drug binding activity, and by my leadership of a team in the NIH/DOE 2021 Petabyte-Scale Sequence Search hack-a-thon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Reconstruction of Fission Product Distribution from Tomographic Scans in TRISO Fuel Graphitic Matrix and Nuclear Grade Graphites

An image reconstruction method was developed to rectify shortcomings of earlier methods that became apparent as destructively sampled data became available. This reconstruction method was applied to the tomographic gamma scans of nuclear graphite and graphitic matrix samples from AGR-3/4. There is generally agreement between profiles measured via destructive sampling of these rings and profiles from tomographic reconstruction.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

A High-Order Discontinuous Galerkin Spectral Element Method for Compressible Reacting Flows

High-order methods have recently been shown to be an effective tool for high-fidelity flow computations like direct numerical simulations and large eddy simulations due to their strong balance between accuracy and computational cost. In this work, a high-order discontinuous Galerkin spectral element method (DGSEM) is developed to solve the chemically reactive Euler equations encountered in high-speed combustion. To handle the disparate length and time scales associated with these equations, we develop a novel method which combines the spectral accuracy of the SEM with the flexibility of DG approach. Thus, the framework is well suited to capture turbulence in smooth regions of the flow, while maintaining numerical stability in the presence of shocks. The numerical method is implemented within the spectral element solver Nek5000. Validation cases are conducted for both non-reactive and reactive discontinuous flows to demonstrate the solver capability. In particular, canonical one-dimensional and two-dimensional detonation simulations are performed and the high-order numerical results are validated against available literature data.

computational fluid dynamics (CFD)↗

DOE OSTI2022

Reconstruction of Fission Product Distribution from Tomographic Scans in TRISO Fuel Graphitic Matrix and Nuclear Grade Graphites

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Improving and Assessing the Quality of Uncertainty Quantification in Deep Learning

Deep learning (DL) models have enjoyed increased attention in recent years because of their powerful predictive capabilities. While many successes have been achieved, standard deep learning methods suffer from a lack of uncertainty quantification (UQ). While the development of methods for producing UQ from DL models is an active area of current research, little attention has been given to the quality of the UQ produced by such methods. In order to deploy DL models to high-consequence applications, high-quality UQ is necessary. This report details the research and development conducted as part of a Laboratory Directed Research and Development (LDRD) project at Sandia National Laboratories. The focus of this project is to develop a framework of methods and metrics for the principled assessment of UQ quality in DL models. This report presents an overview of UQ quality assessment in traditional statistical modeling and describes why this approach is difficult to apply in DL contexts. An assessment on relatively simple simulated data is presented to demonstrate that UQ quality can differ greatly between DL models trained on the same data. A method for simulating image data that can then be used for UQ quality assessment is described. A general method for simulating realistic data for the purpose of assessing a model’s UQ quality is also presented. A Bayesian uncertainty framework for understanding uncertainty and existing metrics is described. Research that came out of collaborations with two university partners are discussed along with a software toolkit that is currently being developed to implement the UQ quality assessment framework as well as serve as a general guide to incorporating UQ into DL applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Time-Lapse Electromagnetic Methods for Monitoring Plume Development in a Carbon Storage Reservoir

Conference presentation at International Meeting for Applied Geoscience & Energy (IMAGE), Houston, Texas, August 25–28, 2025. The Energy & Environmental Research Center (EERC) is leading applied research on electromagnetic (EM) monitoring methods at an active carbon storage site in North Dakota. Injection operations at the site began in February 2024, with a permitted injection rate of up to 2.7 million tonnes of CO 2 annually using six injection wells. CO 2 is captured on-site and injected into the Broom Creek Formation, a predominantly sandstone reservoir and saline aquifer located at a depth of approximately 1800 meters. The EERC led acquisition of multiple active- and passive-source EM techniques between August and October of 2024 to provide a thorough understanding of the resistivity profile at the site.

02 PETROLEUM↗

DOE OSTI2020

Online Modelling and Optimization of Nonlinear Integrable Systems

Nonlinear integrable optics was recently proposed as a design approach to increase the limits on beam brightness and intensity imposed by fast collective instabilities. To study these systems experimentally, a new research electron and proton storage ring, the Integrable Optics Test Accelerator, was constructed and recently commissioned at Fermilab. Beam-based diagnostics and online modelling of nonlinear systems presents unique challenges - in this paper, we report on our efforts to develop optimization methods suited for such lattices. We explore the effectiveness of neural networks as fast online surrogate estimators, and integrate them into a beam-based tuning algorithm. We also develop a method of knob dimensionality reduction and subsequent robust multivariate optimization for maximizing key performance metrics under complicated lattice optics constraints.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Dislocation half-loop control for optimal V-defect density in GaN-based light emitting diodes

V-defects are morphological defects that typically form on threading dislocations during epitaxial growth of $(0001)$-oriented GaN layers. A V-defect is a hexagonal pyramid-shaped depression with six {$10\bar{1}1$}-oriented sidewalls. These semipolar sidewalls have a lower polarization barrier than the polarization barriers present between the polar c-plane quantum wells and quantum barriers and can laterally inject carriers directly into quantum wells in GaN-based light emitting diodes (LEDs). This is especially important, as the high polarization field in c-plane GaN is a significant factor in the high forward voltage of GaN LEDs. The optimal V-defect density for efficient lateral carrier injection in a GaN LED (∼10 9 cm −2 ) is typically an order of magnitude higher than the threading dislocation density of GaN grown on patterned sapphire substrates (∼10 8 cm −2 ). Pure-edge dislocation loops have been known to exist in GaN, and their formation into large V-defects via low-temperature growth with high Si-doping has recently been studied. Here, in this work, we develop a method for pure-edge threading dislocation half-loop formation and density control via disilane flow, growth temperature, and thickness of the half-loop generation layer. We also develop a method of forming the threading dislocation half-loops into V-defects of comparable size to those originating from substrate threading dislocations.

Crystallographic defects↗

DOE OSTI2023

An energy-optimization method to study gel-swelling in confinement

Using our open-source programming environment Morpho, an energy-optimization method is developed to compute equilibrium shapes of an arbitrarily confined swollen hydrogel. The internal strains and contact forces are measured, probing its mechanics.

Joshi, Chaitanya↗

DOE OSTI2026

Throughput Estimation of Data Transport Networks From Digital Twin Measurements

Digital twins of networked infrastructures, known as Virtual Infrastructure Twins (VITs), are increasingly used for software development, pre-deployment testing, and design space exploration. While VITs avoid the costs and potential disruptions associated with experiments on operational networks, their throughput measurements are typically not sufficiently accurate for performance profiling of wide-area networks that they emulate. Here, machine learning (ML) methods are developed to transform these inaccurate VIT network throughput measurements to closely match in peak and overall profile of those from a physical testbed or production network. First, a micro kernel network reflecting a physical network is utilized to collect one-time measurements on a host to support this ML transformation. Then, a generic multi-modal ML method is developed to learn a map that transforms measurements from subsequent VITs on the same host to match past, current and follow-on testbed and cloud networks. ML generalization equations are derived to establish its correctness and probabilistically guarantee its generalization accuracy. Experimental results are presented for a variety of VIT hosts with target testbed and cloud networks; they include a case study of a four-site science ecosystem wherein inaccurate convex VIT measurement profiles are transformed into accurate concave profiles of target networks.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Findings on Subtask 3.1 - Bakken Rich Gas Enhanced Oil Recovery Project

Total in-place oil for the Bakken petroleum system (BPS) (which includes the Bakken and Three Forks Formations) has been estimated to be 600 billion barrels (bbl). However, BPS wells have decline rates as high as 85% over the first 3 years of their lives, and primary recovery factors typically range from 3% to 10% of original oil in place. Given the low initial recovery rates, even small incremental productivity improvements could dramatically increase technically recoverable oil in the BPS. One potential solution is enhanced oil recovery (EOR) using gas injection, such as carbon dioxide (CO2) or hydrocarbon (HC) gases. While commonly used in conventional reservoirs, CO2 EOR in unconventional tight oil reservoirs has been limited to pilot tests. EOR using rich gas (mixture of methane, ethane, and propane) has also been employed in numerous pilots in several unconventional plays and has recently been successfully applied in the Eagle Ford play. If successful, large-scale gas-based EOR in the BPS could dramatically increase oil productivity and recovery factors and extend the life of the play for decades. While CO2 may be a technically suitable working fluid for EOR in the BPS, supplies are limited and costs for using CO2 in EOR pilots are prohibitively high. Meanwhile, produced gas flaring has presented challenges for BPS operators in North Dakota. Analysis conducted by the North Dakota Pipeline Authority indicates that the current gas-gathering infrastructure in North Dakota is insufficient to accommodate all of the associated gas that is produced from the BPS. The geographically isolated location of North Dakota relative to large natural gas markets, combined with suppressed natural gas prices, has made it economically challenging for industry to invest capital in expanding gas-gathering infrastructure in the state. These circumstances led to a research program conducted by the Energy & Environmental Research Center (EERC) in partnership with Liberty Resources Management Company LLC (LR) to examine the potential to use rich gas injection for EOR and mitigate flaring. A rich gas EOR pilot test was designed and executed by LR at its Stomping Horse development area in Williams County, North Dakota. From July 2018 through May 2019, a total of 160 million standard cubic feet (MMscf) of rich produced gas was injected into the BPS using five different wells in a sequential injection strategy. LR’s Leon–Gohrick drill spacing unit (DSU) was used as the test site. Regulatory oversight was provided by the North Dakota Industrial Commission (NDIC). Technical support was provided by the EERC through a series of laboratory, modeling, and field-based activities, and additional post-pilot research activities incorporated learnings from the test, developed new laboratory data, improved fracture modeling methods, and developed machine learning and big data analytics. The results from the Stomping Horse rich gas EOR pilot activities indicate that developing an effective, economical EOR approach for the BPS will require more field tests. Another key lesson learned from the Stomping Horse tests is that detailed pre- and posttest data on reservoir conditions and fluids production are essential. Robust reservoir characterization provides information that is crucial to creating realistic geomodels and conducting valid dynamic simulations of potential EOR scenarios. A detailed understanding of the completions and production history of offset wells is also necessary for valid test result interpretations. This knowledge is essential to designing the operational parameters of injectivity tests and interpreting the results. A conformance control strategy is also essential to success. Laboratory-based examinations of rich gas interactions with reservoir fluids and rocks were conducted, with an emphasis on determining the ability to mobilize oil in the tight reservoir rocks and shales of the BPS. Injection fluid composition was shown to have a positive impact on reducing reservoir oil minimum miscibility pressure (MMP), reducing interfacial tension (IFT), and altering wettability. IFT and contact angle measurements demonstrated that wettability can be altered in the presence of rich gas, suggesting the potential to improve oil recovery. Iterative modeling of surface infrastructure and reservoir performance using data generated by the various project activities was conducted. A geologic model of the Stomping Horse area was built; history-matched oil, gas, and water production was used in simulations of various EOR scenarios. Early programmatic modeling results were used to support LR’s design and operation of the EOR pilot and to provide insight regarding optimization of future commercial-scale BPS EOR design and operations. Post-pilot modeling focused on alternative methods of understanding complex fracture networks and accelerating simulation time. These led to improved simulation run times and provide excellent history-matching results. Several of these iterative models were used as the bases for developing algorithms into machine learning and big data analytics. History matching in reservoir simulation is time-consuming and computer processing-intensive. Machine learning algorithms were created, and an automated history-matching tool was developed. A large set of synthetic reservoir simulations were created to generate well responses (oil, gas, and water production, well bottomhole pressure [BHP], and tracer or propane breakthrough) for a set of EOR operating parameters that included offset well status (open or closed), injectate (rich gas or propane), injection rate, and injection well BHP. A user interface was developed to provide real-time visualization. Machine learning-based models were developed to provide rapid forecasting of well performance given a set of user-defined EOR operating parameters. These predictive models allow the user to modify the offset well status, injection rate, and injection well BHP and rapidly forecast future production performance. The combination of real-time visualization tools with real-time forecasting tools provides a framework for real-time control—operational changes that the EOR site operator can enact (e.g., changing gas injection rates) to affect the observed performance and potentially improve the EOR outcome. There is great reason to be optimistic about the future of EOR in the Bakken. The results of the laboratory studies suggest significant potential for high rates of oil mobilization using produced field gas injection under the right conditions. The results of the lab studies, combined with rigorous statistical analysis of well production data and associated modeling efforts, confirm the notion that fluid mobility within the reservoir is controlled by fractures. As more knowledge is gained about the nature and distribution of fracture networks in the Bakken, the industry will be in a better position to predict and, ultimately, influence fluid mobility. New field tests are necessary to develop a more complete understanding of those conditions. Thoughtful and creatively engineered field tests within a well-characterized geologic setting will yield the fundamental knowledge needed to take Bakken oil production to the next level. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission’s Oil and Gas Research Program and Computer Modelling Group.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2023

Analyzing Hardware and Software Common Cause Failures in Digital Instrumentation and Control Systems using Dual Error Propagation Method

This paper develops a methodology for quantifying software common cause failures (CCFs) in digital instrumentation and control (I&C) systems of nuclear power plants. To support the transition of analog I&C systems to digital in nuclear power plants, probabilistic risk assessment (PRA) techniques are used. The hardware components of the I&C systems have reliability databases that can be used in the PRA studies. However, the failure data for redundant software components of the systems is sparse. Failure of components constitutes a CCF, wherein two or more components or systems fail due to a single shared cause and coupling mechanism. This paper proposes a quantification approach that can simultaneously model hardware and software components, incorporate the CCFs of software systems in the models, and bridge the gap between the failure quantification of models and the development of CCF parametric databases. We demonstrate the dual error propagation method (DEPM) by developing I&C systems failure models for a representative digital reactor trip system. The DEPM models are built to simulate the control and data flows within the systems and can accommodate failure states. By expanding DEPM to software CCFs, we generated alpha factor parameter estimates for each of the modeled error propagation mechanisms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Development of a tomographic reconstruction method for axisymmetric D α emission profiles in the ITER plasma boundary

A tomographic method for reconstructing the axially symmetric D α emission profile in the ITER scrape-off layer and divertor from D α intensity measurements in the fields of view (FoV) of Vis/IR TV and Divertor Impurity Monitor diagnostics is under development. The method takes into account the strong background signal due to stray light from divertor produced by reflections from the metal wall of the vacuum chamber. The method allows to filter out the reflections in D α signals measured in the main chamber. Here, the accuracy of this method is tested within the framework of a synthetic diagnostic, which uses the Raysect and Cherab numerical codes for ray-tracing simulations. The D α emission profiles, simulated with the SOLPS and OEDGE codes, are used as synthetic experimental data. Uncertainty in light reflection properties of the first wall (FW) is the major factor affecting the accuracy of the D α emission reconstruction. The dependence on the uncertainty in the FW surface roughness and on the ratio of diffusive to specular reflection of the error in recovering useful D α signals (the direct light without reflections) in the FoV of the ITER main chamber H-alpha and Visible Spectroscopy Diagnostic is obtained.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Protection Against Graph-Based False Data Injection Attacks on Power Systems

Graph signal processing (GSP) has emerged as a powerful tool for practical network applications, including power system monitoring. By representing power system voltages as smooth graph signals, recent research has focused on developing GSP-based methods for state estimation, attack detection, and topology identification. Included, efficient methods have been developed for detecting false data injection (FDI) attacks, which until now were perceived as non-smooth with respect to the graph Laplacian matrix. Consequently, these methods may not be effective against smooth FDI attacks. In this paper, we propose a graph FDI (GFDI) attack that minimizes the Laplacian-based graph total variation (TV) under practical constraints. In addition, we develop a low-complexity algorithm that solves the non-convex GDFI attack optimization problem using ell_1-norm relaxation, the projected gradient descent (PGD) algorithm, and the alternating direction method of multipliers (ADMM). We then propose a protection scheme that identifies the minimal set of measurements necessary to constrain the GFDI output to high graph TV, thereby enabling its detection by existing GSP-based detectors. Our numerical simulations on the IEEE-57 bus test case reveal the potential threat posed by well-designed GSP-based FDI attacks. Moreover, we demonstrate that integrating the proposed protection design with GSP-based detection can lead to significant hardware cost savings compared to previous designs of protection methods against FDI attacks.

Morgenstern, Gal↗

DOE OSTI2021

Development of New Experimental Methods for Correlated Operando Surface/Gas Characterization

The predictive understanding of catalytic surface reactions requires accurate microkinetic models, and while decades of work has been devoted to the elucidation of the reaction steps in these models, many open questions remain. One key issue is a lack of approaches enabling the local spatially resolved assessment of catalytic activity over a surface. In this report, we detail efforts to develop a new diagnostic approach to solve this problem. The approach is based upon laser resonance enhanced multiphoton ionization of reaction products emitted into the gas phase followed by spatially resolved imaging of the resultant ions or electrons. Ion imaging is pursued with a velocity-selected spatially resolved ion imaging microscope, while electron imaging was attempted in a low energy electron microscope. Successful demonstration of the ion imaging microscope coupled with the development of transport simulations shows promise for a revolutionary new tool to assess local catalytic activity

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Hybrid Cyber-attack Detection in Photovoltaic Farms

Here, to address the cyber-physical security in PV farms, a hybrid cyber-attack detection is proposed in this manuscript. To secure PV farms, the proposed method integrates model-based and data-driven methods by fusing the detection score at the device and system levels. First, a model-based cyber-attack detection method is developed for each PV inverter. A residual between the estimation of the Kalman filter and measurement is calculated. By leveraging the calculated residual from all inverters, a squared Mahalanobis distance is developed for device detection score generation. At the system level, a convolutional neural network (CNN) is proposed to detect cyber-attack using the waveform data at the point of common coupling (PCC) in PV farms. To improve the CNN detection accuracy, a set of well-designed features are extracted from the raw waveform data. Finally, a weighted detection score fusion method is proposed to combine device and system detection scores by using their complementary strength. The feasibility and robustness of the proposed method are validated by testing cases and a comparative experiment.

14 SOLAR ENERGY↗

DOE OSTI2022

Layer Time Control for Large Scale Additive Manufacturing Using High Performance Computing

This work proposes to optimize an additive manufacturing AM process to reduce energy and printing cost. The polymer AM process is inherently dependent on the time-temperature history of each layer to maintain geometric tolerances and mechanical integrity. Our preliminary study shows that regression-based layer time control model using thermal images could result in up to 30% build time reduction for simple geometries. This proposed work would use high-performance computing (HPC) to couple the data-driven model with thermal simulation for better predicting layer temperature profiles, improving throughput of large-scale additive manufacturing, and reducing its energy cost. We have developed a method to optimize a layer deposition time (a.k.a. layer time) for large-scale AM via physics-based simulations. A long layer time leads to an over-cooled surface on which a new layer is deposited, and therefore, it may result in a weak bonding or debonding between layers, cracking, or warping. A short layer time leads to a high temperature of the structure due to insufficient cooling, and therefore, the structure may not be stiff enough and may collapse during manufacturing. Therefore, it is important to estimate the optimal layer time in additive manufacturing for a high-quality product. The temperature of a top layer right before deposition is recommended to be slightly higher than the glass temperature of the material. A temperature cooling was approximated to an exponential function of time, and the optimized layer time was obtained based on a target temperature while maintaining a minimal printing time. The material used is carbon fiber-reinforced polycarbonate (CF/PC), and the large-scale deposition system used is LSAM TM from Thermwood Corporation. Three different layer time cases were used for experiments, and a series of thermal images were obtained via an infra-red (IR) camera during the entire AM processes. AM process simulations were performed using a finite element method and the temperature profiles from the simulation were in good agreements with those from experiments. The layer time optimization was performed based on the temperature profiles from the simulations. A layer temperature with the optimal layer time was confirmed as the target temperature through simulation. In addition to the development of a layer time optimization method, we have developed a numerical framework for AM simulation with element activations in sync with toolpath, based on an open source finite element framework, DEAL.II. A major portion of this work was presented at SAMPE 2022 Conference and Exhibition on May 2022, and published in Proceedings of SAMPE 2022.

42 ENGINEERING↗

DOE OSTI2023

Machine learning methods for particle stress development in suspension Poiseuille flows

Numerical simulations are used to study the dynamics of a developing suspension Poiseuille flow with monodispersed and bidispersed neutrally buoyant particles in a planar channel, and machine learning is applied to learn the evolving stresses of the developing suspension. The particle stresses and pressure develop on a slower time scale than the volume fraction, indicating that once the particles reach a steady volume fraction profile, they rearrange to minimize the contact pressure on each particle. Here we consider how the stress development leads to particle migration, time scales for stress development, and present a new physics-informed Galerkin neural network that allows for learning the particle stresses when direct measurements are not possible. The particle fluxes are compared with the Suspension Balance Model with good agreement. We show that when stress measurements are possible, the MOR-physics operator learning method can also capture the particle stresses.

97 MATHEMATICS AND COMPUTING↗