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At least 127 records · Page 7

A computational modeling framework for pre-clinical evaluation of cardiac mapping systems

There are a variety of difficulties in evaluating clinical cardiac mapping systems, most notably the inability to record the transmembrane potential throughout the entire heart during patient procedures which prevents the comparison to a relevant “gold standard”. Cardiac mapping systems are comprised of hardware and software elements including sophisticated mathematical algorithms, both of which continue to undergo rapid innovation. The purpose of this study is to develop a computational modeling framework to evaluate the performance of cardiac mapping systems. The framework enables rigorous evaluation of a mapping system’s ability to localize and characterize (i.e., focal or reentrant) arrhythmogenic sources in the heart. The main component of our tool is a library of computer simulations of various dynamic patterns throughout the entire heart in which the type and location of the arrhythmogenic sources are known. Our framework allows for performance evaluation for various electrode configurations, heart geometries, arrhythmias, and electrogram noise levels and involves blind comparison of mapping systems against a “silver standard” comprised of computer simulations in which the precise transmembrane potential patterns throughout the heart are known. A feasibility study was performed using simulations of patterns in the human left atria and three hypothetical virtual catheter electrode arrays. Activation times (AcT) and patterns (AcP) were computed for three virtual electrode arrays: two basket arrays with good and poor contact and one high-resolution grid with uniform spacing. The average root mean squared difference of AcTs of electrograms and those of the nearest endocardial action potential was less than 1 ms and therefore appears to be a poor performance metric. In an effort to standardize performance evaluation of mapping systems a novel performance metric is introduced based on the number of AcPs identified correctly and those considered spurious as well as misclassifications of arrhythmia type; spatial and temporal localization accuracy of correctly identified patterns was also quantified. This approach provides a rigorous quantitative analysis of cardiac mapping system performance. Proof of concept of this computational evaluation framework suggests that it could help safeguard that mapping systems perform as expected as well as provide estimates of system accuracy.

59 BASIC BIOLOGICAL SCIENCES↗

Mining data in a dynamic PRA framework

Computational (also known as Dynamic) Probabilistic Risk Assessment (PRA) methods employs system simulation codes coupled with stochastic analysis tools in order to determine probabilities of certain outcomes such as system failure. In contrast to classical PRA methods (i.e., Event-Tree and Fault-Tree) in which timing and sequencing of events is set by the analyst, accident progression is dictated by the system control logic and its interaction with system temporal evolution. Due to the nature of the problem, Simulation-Based PRA methods require large amount of computationally expensive simulation runs. In addition, these methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). In this paper we investigate and apply several methods and algorithms to analyze these large amounts of time-dependent data. Furthermore, the scope of this article is to present a broad overview of methods and algorithms that can be used to improve data quality and to analyze and extract information from large data sets containing time dependent data. In this context, “extracting information” means constructing input-output correlations, finding commonalities, and identifying outliers.

97 MATHEMATICS AND COMPUTING↗

Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS - Version 0.21 (20200601)

The continental flood inundation mapping (CFIM) framework is a high-performance computing (HPC)-based computational framework for the Height Above Nearest Drainage (HAND)-based inundation mapping methodology. Using the 10m Digital Elevation Model (DEM) data produced by U.S. Geological Survey (USGS) 3DEP (the 3-D Elevation Program) and the NHDPlus hydrography dataset produced by USGS and the U.S. Environmental Protection Agency (EPA), a hydrological terrain raster called HAND is computed for HUC6 units in the conterminous U.S. (CONUS). The value of each raster cell in HAND is an approximation of the relative elevation between the cell and its nearest water stream. Derived from HAND, a hydraulic property table is established to calculate river geometry properties for each of the 2.7 million river reaches covered by NHDPlus (5.5 million kilometers in total length). This table is a lookup table for water depth given an input stream flow value. Such lookup is available between water depth 0m and 25m at 1-foot interval. The flood inundation map is then computed by using HAND and this lookup table based on the near real-time water forecast from the National Water Model (NWM) at the National Oceanic and Atmospheric Administration (NOAA). HAND and the Hydraulic Property Table version v0.21 is an upgrade to v0.2. Version 0.21 applies NHD HR etching to DEMs for all HUC6 units before running the HAND workflow. This new version also fixed the issue of void areas along HUC boundary. This dataset comprises 331 HUC6 units for CONUS (excluding the five great lakes units), each is a downloadable zip file. Version 0.1 was computed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urban-Champaign in 2016 and is currently hosted at the Texas Advanced Computing Center (TACC). Please cite this data DOI and the following publications and data DOIs when you use HAND and the hydraulic property table: Liu, Yan Y. Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS - Version 0.2. (20200301). Oak Ridge Leadership Computing Facility. (2020). DOI: 10.13139/ORNLNCCS/1608331 Liu, Yan Y., David R. Maidment, David G. Tarboton, Xing Zheng, and Shaowen Wang. 'A CyberGIS integration and computation framework for high-resolution continental-scale flood inundation mapping.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 770-784. DOI: 10.1111/1752-1688.12660 Zheng, Xing, David G. Tarboton, David R. Maidment, Yan Y. Liu, and Paola Passalacqua. 'River channel geometry and rating curve estimation using height above the nearest drainage.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 785-806. DOI: 10.1111/1752-1688.12661 Liu, Y. (2018). Height Above Nearest Drainage (HAND) for CONUS, HydroShare, https://doi.org/10.4211/hs.69f7d237675c4c73938481904358c789 LICENSE FOR USE -- MAPS AND DATA DISCLAIMER This resource is shared under the Creative Commons Attribution CC BY, http://creativecommons.org/licenses/by/4.0/ MAPS AND DATA DISCLAIMER The Oak Ridge National Laboratory (ORNL) shall not be held liable for improper or incorrect use of the data described or information contained on this map or associated series of maps. The data and related map graphics are not legal, land survey or engineering documents and are not intended to be used as such. ORNL gives no warranty, express or implied, as to the accuracy, reliability, utility or completeness of this information. The user of these maps and data assumes all responsibility and risk for the use of the maps and data. ORNL disclaims all warranties, representations or endorsements either express or implied, with regard to the information contained in this map product, including, but not limited to, all implied warranties of merchantability, fitness for a particular purpose or non-infringement. This preliminary map product is for research and review purposes only. It is not intended to be used for emergency management operational or life safety decisions at the local or regional governmental level or by the general public. Users requiring information regarding hazardous conditions or meteorological conditions for specific geographic areas should consult directly with their city or county emergency management office.

54 ENVIRONMENTAL SCIENCES↗

Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS

The continental flood inundation mapping (CFIM) framework is a high-performance computing (HPC)-based computational framework for the Height Above Nearest Drainage (HAND)-based inundation mapping methodology. Using the 10m Digital Elevation Model (DEM) data produced by U.S. Geological Survey (USGS) 3DEP (the 3-D Elevation Program) and the NHDPlus hydrography dataset produced by USGS and the U.S. Environmental Protection Agency (EPA), a hydrological terrain raster called HAND is computed for HUC6 units in the conterminous U.S. (CONUS). The value of each raster cell in HAND is an approximation of the relative elevation between the cell and its nearest water stream. Derived from HAND, a hydraulic property table is established to calculate river geometry properties for each of the 2.7 million river reaches covered by NHDPlus (5.5 million kilometers in total length). This table is a lookup table for water depth given an input stream flow value. Such lookup is available between water depth 0m and 25m at 1-foot interval. The flood inundation map is then computed by using HAND and this lookup table based on the near real-time water forecast from the National Water Model (NWM) at the National Oceanic and Atmospheric Administration (NOAA). HAND and the Hydraulic Property Table version 0.2. is created to correspond to data updates in the USGS 1/3 arcsec DEM, the USGS National Hydrography Dataset, including its Water Boundary Dataset, and the NHDPlus medium resolution dataset. This dataset comprises 331 HUC6 units for CONUS (excluding the five great lakes units), each is a downloadable zip file. Version 0.1 was computed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urban-Champaign in 2016 and is currently hosted at the Texas Advanced Computing Center (TACC). Please cite this data DOI and the following publications and data DOIs when you use HAND and the hydraulic property table: Liu, Yan Y., David R. Maidment, David G. Tarboton, Xing Zheng, and Shaowen Wang. 'A CyberGIS integration and computation framework for high-resolution continental-scale flood inundation mapping.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 770-784. DOI: 10.1111/1752-1688.12660 Zheng, Xing, David G. Tarboton, David R. Maidment, Yan Y. Liu, and Paola Passalacqua. 'River channel geometry and rating curve estimation using height above the nearest drainage.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 785-806. DOI: 10.1111/1752-1688.12661 Liu, Y. (2018). Height Above Nearest Drainage (HAND) for CONUS - v0.1, HydroShare, https://doi.org/10.4211/hs.69f7d237675c4c73938481904358c789 LICENSE FOR USE -- MAPS AND DATA DISCLAIMER This resource is shared under the Creative Commons Attribution CC BY, http://creativecommons.org/licenses/by/4.0/ MAPS AND DATA DISCLAIMER The Oak Ridge National Laboratory (ORNL) shall not be held liable for improper or incorrect use of the data described or information contained on this map or associated series of maps. The data and related map graphics are not legal, land survey or engineering documents and are not intended to be used as such. ORNL gives no warranty, express or implied, as to the accuracy, reliability, utility or completeness of this information. The user of these maps and data assumes all responsibility and risk for the use of the maps and data. ORNL disclaims all warranties, representations or endorsements either express or implied, with regard to the information contained in this map product, including, but not limited to, all implied warranties of merchantability, fitness for a particular purpose or non-infringement. This preliminary map product is for research and review purposes only. It is not intended to be used for emergency management operational or life safety decisions at the local or regional governmental level or by the general public. Users requiring information regarding hazardous conditions or meteorological conditions for specific geographic areas should consult directly with their city or county emergency management office.

54 ENVIRONMENTAL SCIENCES↗

A rotorcraft in-flight ice detection framework using computational aeroacoustics and Bayesian neural networks

Abstract This work develops a novel ice detection framework specifically suitable for rotorcraft using computational aeroacoustics and Bayesian neural networks. In an offline phase of the work, the acoustic signature of glaze and rime ice shapes on an oscillating wing are computed. In addition, the aerodynamic performance indicators corresponding to the ice shapes are also monitored. These performance indicators include the lift, drag, and moment coefficients. A Bayesian neural network is subsequently trained using projected Stein variational gradient descent to create a mapping from the acoustic signature generated by the iced wings to predict their performance indicators along with quantified uncertainty that is highly important for time- and safety-critical decision-making scenarios. While the training is carried out fully offline, usage of the Bayesian neural network to make predictions can be conducted rapidly online allowing for an ice detection system that can be used in real time and in-flight.

42 ENGINEERING↗

A Novel Modeling Framework for Computationally Efficient and Accurate Real-Time Ensemble Flood Forecasting With Uncertainty Quantification

A novel modeling framework that simultaneously improves accuracy, predictability, and computational efficiency is presented. It embraces the benefits of three modeling techniques integrated together for the first time: surrogate modeling, parameter inference, and data assimilation. The use of polynomial chaos expansion (PCE) surrogates significantly decreases computational time. Parameter inference allows for model faster convergence, reduced uncertainty, and superior accuracy of simulated results. Ensemble Kalman filters assimilate errors that occur during forecasting. To examine the applicability and effectiveness of the integrated framework, we developed 18 approaches according to how surrogate models are constructed, what type of parameter distributions are used as model inputs, and whether model parameters are updated during the data assimilation procedure. We conclude that (1) PCE must be built over various forcing and flow conditions, and in contrast to previous studies, it does not need to be rebuilt at each time step; (2) model parameter specification that relies on constrained, posterior information of parameters (so-called Selected specification) can significantly improve forecasting performance and reduce uncertainty bounds compared to Random specification using prior information of parameters; and (3) no substantial differences in results exist between single and dual ensemble Kalman filters, but the latter better simulates flood peaks. The use of PCE effectively compensates for the computational load added by the parameter inference and data assimilation (up to ~80 times faster). Therefore, the presented approach contributes to a shift in modeling paradigm arguing that complex, high-fidelity hydrologic and hydraulic models should be increasingly adopted for real-time and ensemble flood forecasting.

54 ENVIRONMENTAL SCIENCES↗

Computational Bayesian Framework for Quantification and Reduction of Predictive Uncertainty in Subsurface Environmental Modeling

Subsurface environmental systems are open and complex, in which intricate hydrologic, microbiologic, and geochemical processes occur and interact at multiple scales. Understanding and predicting system responses to natural forces (e.g., climate changes) and human activities (e.g., contaminant remediation and CO 2 sequestration) is indispensable for managing water resources, cleaning subsurface contamination at many sites of the Department of Energy (DOE), and providing expert analysis to inform policy-making on long-term stewardship of nuclear waste disposal and CO 2 storage sites. Groundwater reactive transport modeling is necessary for understanding and predicting the complex subsurface environmental system. However, as complex systems are never completely predictable, model predictions of the subsurface system are inherently uncertain, and uncertainty is one of the greatest obstacles in simulating the subsurface environment. Quantifying predictive uncertainty of the complex system is critical to test model predictive power, support decision-making, and guide experimental design and data collection for uncertainty reduction. This project tackled two major obstacles to efficient and effective quantification and reduction of predictive uncertainty in simulating the complex subsurface environment. One obstacle is that existing methods of uncertainty quantification are too fragmented and incomplete for understanding and predicting the complex subsurface environment as a whole. The other obstacle is that existing methods of uncertainty quantification are computationally demanding and may not be applicable to groundwater reactive transport modeling that is always computationally expensive. The above two obstacles to uncertainty quantification directly affect the design of data collection schemes for uncertainty reduction. In this project, we developed a comprehensive Bayesian framework to remove the first obstacle. The second obstacle was tackled by using the sparse grid methods, which were originally developed and analyzed for numerical integration in the field of applied mathematics. We integrated the sparse grid methods into the Bayesian framework seamlessly, which led to a sparse-grid-based method of Bayesian uncertainty analysis. The developed computational Bayesian framework has been applied to a number of subsurface environmental problems through collaborating with scientists at the Pacific Northwest National Laboratory and Oak Ridge National Laboratory. The applications demonstrated that the computational Bayesian framework is general and compatible with any models and numerical codes of subsurface modeling. It is thus can be applied to gain insights for subsurface environmental modeling. This project helped the PI achieve his career goal to advance the state-of-the-art computational methods in uncertainty quantification for subsurface environmental modeling. This project supported two doctoral students, two master students, and one post-doc. The two doctoral students, after their graduation, worked as post-docs at the Pacific Northwest National Laboratory and the Oak Ridge National Laboratory. The project produced a total of 29 journal articles (four under review), one book chapter, and a number of conference proceedings and abstracts.

54 ENVIRONMENTAL SCIENCES↗

ChemComp: A Compilation Framework for Computing with Chemical Reaction Networks

The acceleration of scientific computation, data analytics, and artificial intelligence is driving a surge in computational requirements. Yet, state-of-the-art high-performance computing systems are approaching physical limitations that impede further significant improvements in energy efficiency. As we move towards post-exascale computing systems, innovative approaches are necessary to overcome this barrier in power consumption. Novel analog and hybrid digital-analog architectures hold promise for enhancing energy efficiency by several orders of magnitude. Biochemical computation stands out among the various solutions being explored due to its potential to enable new classes of devices with immense computational capabilities. These devices can capitalize on the inherent efficacy of biological cells in solving optimization problems and are scalable through increasing reaction system size or vessel capacity, potentially satisfying scientific computing's high-performance requirements. Nonetheless, several theoretical and practical limitations persist, including problem formulation and mapping to chemical reaction networks (CRNs) and implementation of actual CRN devices. In this paper, we propose a framework for biochemical computation using systems chemistry. We present the initial components of our approach: an abstract chemical reaction dialect implemented as a multi-level intermediate representation (MLIR) compiler extension and a pathway to represent mathematical problems with CRNs. To showcase the potential of this approach, we emulate a simplified chemical reservoir device. This work lays the groundwork for leveraging chemistry's computing potential in creating energy-efficient, high-performance computing systems tailored to contemporary computational needs.

artificial intelligence↗

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗

dV/dt - Accelerating the Rate of Progress towards Extreme Scale Collaborative Science

This report introduces publications that report the results of a project that aimed to design a computational framework that enables computational experimentation at scale while supporting the model of “submit locally, compute globally”. The project focuses on estimating application resource needs, finding the appropriate computing resources, acquiring those resources,deploying the applications and data on the resources, managing applications and resources during run.

97 MATHEMATICS AND COMPUTING↗

Advanced Methods for Immersed Domain Multi-physics Computations

This is the final report on the project, and describes the main accomplishments in the development of the Shifted Boundary Method (SBM), a new computational framework for embedded/immersed computational mechanics applications.

97 MATHEMATICS AND COMPUTING↗

Fatigue life prediction of powder bed fused–laser beam AlSi10Mg: Incorporating critical defects via crystal plasticity modelling

The current study provides a microstructurally-based computational framework to predict the fatigue life of additive manufactured (AM), i.e., powder bed fused–laser beam (PBF-LB), AlSi10Mg specimens using the crystal plasticity finite element method (CPFEM). The fractography analysis, electron backscatter diffraction (EBSD), uniaxial and cyclic responses, and fatigue life of specimens were used to inform the computational framework. CPFE simulation was used to compute fatigue indicator parameters (FIPs) as fatigue driving forces. A new fatigue criterion is introduced based on FIPs, which was calibrated using experimental fatigue data. The proposed fatigue measure was evaluated versus the specimens with critical defects of various sizes and locations subjected to different stress amplitudes. The results show that the developed framework can capture the fatigue life of samples with different critical defect locations and sizes along with different stress amplitudes for both high-cycle fatigue (HCF) and very high-cycle fatigue (VHCF) regimes.

Additive manufacturing↗

Assessment of Current MACCS Capabilities for Modeling Atmospheric Physical and Chemical Transformations

The physical and chemical transformation during atmospheric transport of radionuclides released into the environment has the possibility of impacting consequence modeling results. Accordingly, this report identifies physical and chemical transformations that may occur following release of chemically reactive radioactive species, how those transformations may affect modeling of consequences of release to the atmosphere and identifies current capabilities – in both MACCS and other state-of-practice atmospheric transport and dispersions models– to model those transformations. It was found that the inclusion of physical and chemical transformations is currently very limited in current state-of-practice codes for atmospheric dispersion of radionuclides. State-of-practice atmospheric dispersion codes appear to be typically limited to simulating either physical-chemical transformations or radioactive transformations, but not both. A state-of-practice atmospheric dispersion code capable of performing parallel physical, chemical, and radioactive transformation was not identified. A few atmospheric dispersion codes capable of modeling physical and chemical transport of specific species such as tritium or uranium hexafluoride were identified. Consequently, there is currently no information available that clearly suggests updates to the MACCS code are needed to bring it up to state-of-practice. However, investigations concluded that the MACCS computational framework can currently accommodate multiple physical/chemical forms in one simulation. Additionally, with some major assumptions, the computational framework in MACCS can accommodate parallel physical-chemical and radioactive transformations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Status of Multiple Channel Fuel Performance Capabilities Within the SAS4A/SASSYS-1 Safety Analysis Software

SAS4A/SASSYS-1 (SAS) is a fast-running simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. It is a critical element of safety analysis capabilities for the U.S. Department of Energy and is utilized within industry to perform the transient safety analyses required to support the licensing of Liquid Metal-cooled Fast Reactors (LMFRs). Although SAS is exceptionally fast for most transient scenarios, fuel performance calculations, along with the associated pre-transient characterization of the fuel pin, may be required for transient scenarios where fuel pin failure is hypothesized. Both the pre-transient characterization and the transient fuel performance calculation are necessary to properly quantify margins to potential fuel failure and assess the time spent potentially exceeding such margins during events. While safety analysis calculations with fuel performance models provide a more detailed characterization of the reactor during a transient, the pre-transient characterization can be time-consuming and computationally expensive. Often, large numbers of fuel pins have been exposed to similar pre-transient irradiation conditions. Similarly, the same pre-transient fuel characterization may be applicable to numerous transient conditions. This provides an opportunity to optimize the SAS computational framework such that pre-transient fuel characterization can be shared across multiple channels (fuel pins) and across multiple simulations, thus dramatically reducing overall computational costs. This report summarizes progress toward enhancing the SAS computational framework to support shared, multiple channel fuel performance characterizations intended to significantly reduce computational costs. Preliminary testing has shown that the computational time saved by using the pre-transient sharing capability is approximately equal to the time it takes to perform the pre-transient characterization.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

ChemGraph as an agentic framework for computational chemistry workflows

Atomistic simulations are essential in chemistry and materials science but remain challenging to run due to the expert knowledge required for the setup, execution, and validation stages of these calculations. We present ChemGraph, an agentic framework powered by artificial intelligence and state-of-the-art simulation tools to streamline and automate computational chemistry and materials science workflows. ChemGraph leverages graph neural network-based foundation models for accurate yet computationally efficient calculations and large language models (LLMs) for natural language understanding, task planning, and scientific reasoning to provide an intuitive and interactive interface. We evaluate ChemGraph across 13 benchmark tasks and demonstrate that smaller LLMs (GPT-4o-mini, Claude-3.5-haiku, Qwen-2.5-14B) perform well on simple workflows, while more complex tasks benefit from using larger models. Importantly, we show that decomposing complex tasks into smaller subtasks through a multi-agent framework enables GPT-4o to reach perfect accuracy and smaller LLMs to match or exceed single-agent GPT-4o's performance in these benchmarks.

Computational chemistry↗