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DOE OSTI2016

CO 2 adsorption-induced structural changes in coordination polymer ligands elucidated via molecular simulations and experiments

Aiming to elucidate guest-induced structural changes in the coordination polymer CPL-2, grand canonical Monte Carlo (GCMC) simulations were used to predict CO 2 loadings in this material, and the results were compared with experimental isotherms. Our calculations suggest that CPL-2 exhibits more pronounced CO 2 -induced structural changes than previously reported. As the initial evidence, the isotherm simulated in the previously reported CPL-2 structure (experimentally resolved from X-ray diffraction in the “as-synthesized” CPL-2) underestimated the measured CO 2 loadings at high pressure, indicating that CPL-2 might undergo structural changes that enable higher pore volumes at high pressure. GCMC simulations in CPL-2 structures considering moderate unit cell expansions reported in the literature still underestimated high-pressure experimental loadings. However, considering an incremental rotation of the CPL-2 bipyridyl pillars with increasing CO 2 pressure, we were able to trace the measured isotherm with the simulation data. Computational analysis shows that ligand rotation in CPL-2 enables higher pore volumes, which, in turn, accommodate more CO 2 as the gas pressure increases. Desorption measurements suggest that hysteresis in the CO 2 isotherm of CPL-2 may also be linked to ligand rotation, and the measured adsorption/desorption cycles show that the rotation is reversible. Based on our simulations for CPL-4 and CPL-5 and previously reported experimental data, it is likely that these materials, which differ from CPL-2 in the bipyridyl ligand, behave similarly in the presence of CO 2 . Our results help understand the behavior of these materials, which present the kind of structural changes that could be potentially exploited to enhance the CO 2 working capacity of ultra-microporous materials for carbon capture applications.

Meza-Morales, Paul J.↗

DOE OSTI2016

Spatial Precision in Magnetic Resonance Imaging–Guided Radiation Therapy: The Role of Geometric Distortion

Because magnetic resonance imaging–guided radiation therapy (MRIgRT) offers exquisite soft tissue contrast and the ability to image tissues in arbitrary planes, the interest in this technology has increased dramatically in recent years. However, intrinsic geometric distortion stemming from both the system hardware and the magnetic properties of the patient affects MR images and compromises the spatial integrity of MRI-based radiation treatment planning, given that for real-time MRIgRT, precision within 2 mm is desired. In this article, we discuss the causes of geometric distortion, describe some well-known distortion correction algorithms, and review geometric distortion measurements from 12 studies, while taking into account relevant imaging parameters. Eleven of the studies reported phantom measurements quantifying system-dependent geometric distortion, while 2 studies reported simulation data quantifying magnetic susceptibility–induced geometric distortion. Of the 11 studies investigating system-dependent geometric distortion, 5 reported maximum measurements less than 2 mm. The simulation studies demonstrated that magnetic susceptibility–induced distortion is typically smaller than system-dependent distortion but still nonnegligible, with maximum distortion ranging from 2.1 to 2.6 mm at a field strength of 1.5 T. As expected, anatomic landmarks containing interfaces between air and soft tissue had the largest distortions. The evidence indicates that geometric distortion reduces the spatial integrity of MRI-based radiation treatment planning and likely diminishes the efficacy of MRIgRT. Better phantom measurement techniques and more effective distortion correction algorithms are needed to achieve the desired spatial precision.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2020

Phase-field simulations of intergranular fission gas bubble behavior in U 3 Si 2 nuclear fuel

U 3 Si 2 is a potential accident-tolerant fuel that shows promise due to its high thermal conductivity and higher uranium density relative to UO 2 . However, its swelling and fission gas release behavior in light water reactor (LWR) conditions is relatively unknown. To provide mechanistic insight and determine parameters for engineering-scale fuel performance modeling of pellet-form U 3 Si 2 , phase-field simulations of the growth, interconnection, and venting of intergranular fission gas bubbles were performed. The fractional coverage of the grain boundary and the fraction of bubble area that is vented were calculated as a function of time. From the simulation data, the fractional grain boundary coverage at saturation, an important parameter needed in engineering-scale modeling of swelling and fission gas release, was determined. Multiple simulations were run to determine the uncertainty in the calculated value. Finally, the effect of model assumptions and input parameters that are not well known was evaluated. Simulation results are compared to related theoretical and computational work. Based on the simulation results, a value of 0.60 for the fractional grain boundary coverage at saturation is recommended for U 3 Si 2 fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

DOE OSTI2023

Recursive Use of the Short-Time Fast Fourier Transform for Signature Analysis in Continuous Processes

Although a nuclear reactor is a hostile environment for sensing and electrical communications, the reactor core is amenable to acoustic communication. An acoustic measurement infrastructure (AMI) has been installed in the Advanced Test Reactor (ATR) to record acoustic signals that can capture its different operating regimes. AMI uses coolant pumps as continuous signal sources, coolant and structural components as transmission lines, and accelerometers to capture system motion. A recursive signal processing technique based on the short-time fast Fourier transform (STFFT) for continuous processes provides unique signatures for diagnostic and prognostic analyses from the system motion data. Here this article presents a recursive STFFT methodology that processes acoustic signals from continuous industrial processes. The article first discusses the initial STFFT use with simulated data to elucidate the basic principles necessary to understand and interpret the STFFT results from actual pump vibration data. Each repetitive use of the STFFT on pump vibration data using the results from the prior STFFT processing will generate additional complimentary time-frequency-based signatures. These signatures are generated by the coolant pumps operating under different process conditions. After each use of the STFFT, the resulting signatures provide exemplary examples of the diversity and intuitive nature of recursively using the STFFT. This article focuses on recursively using the STFFT to provide numerous complimentary and diverse signatures that will ultimately be inputs for machine learning algorithms that provide predictive data analytics. The intuitive nature of the information and signatures from recursive STFFT processing will also bring intuitive interpretation capabilities to machine learning and predictive data analytic techniques.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

InSituNet: Deep Image Synthesis for Parameter Space Exploration of Ensemble Simulations

We propose InSituNet, a deep learning based surrogate model to support parameter space exploration for ensemble simulations that are visualized in situ. In situ visualization, generating visualizations at simulation time, is becoming prevalent in handling large-scale simulations because of the I/O and storage constraints. However, in situ visualization approaches limit the flexibility of post-hoc exploration because the raw simulation data are no longer available. Although multiple image-based approaches have been proposed to mitigate this limitation, those approaches lack the ability to explore the simulation parameters. Our approach allows flexible exploration of parameter space for large-scale ensemble simulations by taking advantage of the recent advances in deep learning. Specifically, we design InSituNet as a convolutional regression model to learn the mapping from the simulation and visualization parameters to the visualization results. With the trained model, users can generate new images for different simulation parameters under various visualization settings, which enables in-depth analysis of the underlying ensemble simulations. We demonstrate the effectiveness of InSituNet in combustion, cosmology, and ocean simulations through quantitative and qualitative evaluations.

deep learning↗

DOE OSTI2020

Mesoscale modeling to inform Bison models of accident tolerant fuel concepts

U 3 Si 2 and doped UO 2 have been under investigation in recent years as potential accident-tolerant fuel concepts. In this report, lower-length scale studies of these fuel concepts carried out during Fiscal Year 2020 are detailed. U 3 Si 2 is a potential accident-tolerant fuel that shows promise due to its high thermal conductivity and higher uranium density relative to UO 2 . However, its swelling and fission gas release behavior in light water reactor (LWR) conditions is relatively unknown. To provide mechanistic insight and determine parameters for engineering-scale fuel performance modeling of pellet-form U 3 Si 2 , phase-field simulations of the growth, interconnection, and venting of intergranular fission gas bubbles were performed. The fractional coverage of the grain boundary and the fraction of bubble area that is vented were calculated as a function of time. From the simulation data, the fractional grain boundary coverage at saturation, an important parameter needed in engineering-scale modeling of swelling and fission gas release, was determined. Multiple simulations were run to determine the uncertainty in the calculated value. The effect of model assumptions and input parameters that are not well known was evaluated. Simulation results are compared to related theoretical and computational work. Based on the simulation results, a value of 0.60 for the fractional grain boundary coverage at saturation is recommended for U 3 Si 2 fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Addressing GPU memory limitations for Graph Neural Networks in High-Energy Physics applications

Introduction Reconstructing low-level particle tracks in neutrino physics can address some of the most fundamental questions about the universe. However, processing petabytes of raw data using deep learning techniques poses a challenging problem in the field of High Energy Physics (HEP). In the Exa.TrkX Project, an illustrative HEP application, preprocessed simulation data is fed into a state-of-art Graph Neural Network (GNN) model, accelerated by GPUs. However, limited GPU memory often leads to Out-of-Memory (OOM) exceptions during training, due to the large size of models and datasets. This problem is exacerbated when deploying models on High-Performance Computing (HPC) systems designed for large-scale applications. Methods We observe a high workload imbalance issue during GNN model training caused by the irregular sizes of input graph samples in HEP datasets, contributing to OOM exceptions. We aim to scale GNNs on HPC systems, by prioritizing workload balance in graph inputs while maintaining model accuracy. Our paper introduces diverse balancing strategies aimed at decreasing the maximum GPU memory footprint and avoiding the OOM exception, across various datasets. Results Our experiments showcase memory reduction of up to 32.14% compared to the baseline. We also demonstrate the proposed strategies can avoid OOM in application. Additionally, we create a distributed multi-GPU implementation using these samplers to demonstrate the scalability of these techniques on the HEP dataset. Discussion By assessing the performance of these strategies as data loading samplers across multiple datasets, we can gauge their effectiveness in both single-GPU and distributed environments. Our experiments, conducted on datasets of varying sizes and across multiple GPUs, broaden the applicability of our work to various GNN applications that handle input datasets with irregular graph sizes.

Lee, Claire Songhyun↗

DOE OSTI2013

Hard x-ray tomographic studies of the destruction of an energetic electron ring

A tomography system was designed and built at the Large Plasma Device to measure the spatial distribution of hard x-ray (100 KeV-3 MeV) emissivity. The x-rays were generated when a hot electron ring was significantly disrupted by a shear Alfven wave. The plasma is pulsed at 1 Hz (1 shot/s). A lead shielded scintillator detector with an acceptance angle defined by a lead pinhole is mounted on a rotary gimbal and used to detect the x-rays. The system measures one chord per plasma shot using only one detector. A data plane usually consists of several hundred chords. A novel Dot by Dot Reconstruction (DDR) method is introduced to calculate the emissivity profile from the line integrated data. In the experiments, there are often physical obstructions, which make measurements at certain angles impossible. The DDR method works well even in this situation. The method was tested with simulated data, and was found to be more effective than previously published methods for the specific geometry of this experiment. The reconstructed x-ray emissivity from experimental data by this method is shown.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

Feature-Based Analysis of Plasma-Based Particle Acceleration Data

Plasma-based particle accelerators can produce and sustain thousands of times stronger acceleration fields than conventional particle accelerators, providing a potential solution to the problem of the growing size and cost of conventional particle accelerators. To facilitate scientific knowledge discovery from the ever growing collections of accelerator simulation data generated by accelerator physicists to investigate next-generation plasma-based particle accelerator designs, we describe a novel approach for automatic detection and classification of particle beams and beam substructures due to temporal differences in the acceleration process, here called acceleration features. The automatic feature detection in combination with a novel visualization tool for fast, intuitive, query-based exploration of acceleration features enables an effective top-down data exploration process, starting from a high-level, feature-based view down to the level of individual particles. We describe the application of our analysis in practice to analyze simulations of single pulse and dual and triple colliding pulse accelerator designs, and to study the formation and evolution of particle beams, to compare substructures of a beam and to investigate transverse particle loss.

43 PARTICLE ACCELERATORS↗

DOE OSTI2015

Data preservation at the Fermilab Tevatron

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and DO experiments each have nearly 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 or beyond. To achieve this, we are implementing a system that utilizes virtualization, automated validation, and migration to new standards in both software and data storage technology as well as leveraging resources available from currently-running experiments at Fermilab. Furthermore, these efforts will provide useful lessons in ensuring long-term data access for numerous experiments throughout high-energy physics, and provide a roadmap for high-quality scientific output for years to come.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2025

Hypersonic wake velocity measurements using acetone molecular tagging velocimetry

Molecular tagging velocimetry, a minimally intrusive laser diagnostic, was used to find quantitative off-body velocity measurements in the wake of both strut-mounted and free-flight spheres in hypersonic flow. Acetone gas seeded in the flow was excited using the fourth harmonic of a pulse-burst Nd:YAG laser. The experimental tests were validated and compared to simulations using a continuous Galerkin flow solver and an adaptive mesh refinement process. Near the centerline in the wake of the sphere, velocities between −105 and 65 m/s were observed due to reverse flow in the viscous shear layer. Similarly, the simulated data showed negative velocity values in the shear layer region. Outside of the shear layer, average velocities of 730 m/s were observed in both the experimental and simulated results. The overall average uncertainty for the strut-mounted and free-flight cases was estimated to have an accuracy of ±4% (±35.5m/s or 4.9%). In conclusion, this non-intrusive technique provides a velocity map of the wake behind a sphere under hypersonic conditions.

42 ENGINEERING↗

DOE OSTI2019

Grid Data Crossing Platform (GriD-Xing)

This project is to develop a data management and analytics platform called Grid Data Crossing (GriD-Xing) that integrates data processing, storage, analysis, and visualization functionalities for users at industry (e.g., EMS and DMS) and universities. It intends to increase the applicability of large set of multi-source data (e.g., SCADA, PMU, μPMU, AMI, inverter, load/DER forecasting, and cyber data) and eventually improve the resilience, reliability, and security of critical energy infrastructure. GriD-Xing also intends to be a research platform to identify the usefulness of large multi-source data via case studies of interest to industry (e.g., 2011 southwest cold weather and 2016 Blue Cut fire events). In the first year, the team focused on the development and demonstration of large multi-source data (e.g., PMU, μPMU, SCADA, AMI, and cyber data) processing, storage, and analysis. Specifically, the team designed GriD-Xing framework in functional and structural aspects, developed GriD-Xing algorithms for large multi-source grid data processing, storage, and analysis, and finally demonstrated GriD-Xing prototype algorithms performance through a series of tests and case studies using real-world and simulation data.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS1995

Non-local transport in turbulent MHD convection

The nonlocal non-diffusive transport of passive scalars in turbulent magnetohydrodynamic (MHD) convection is investigated using transilient matrices. These matrices describe the probability that a tracer particle beginning at one position in a flow will be advected to another position after some time. A method for the calculation of these matrices from simulation data which involves following the trajectories of passive tracer particles and calculating their transport statistics, is presented. The method is applied to study the transport in several simulations of turbulent, rotating, three dimensional compressible, penetrative MDH convection. Transport coefficients and other diagnostics are used to quantify the transport, which is found to resemble advection more closely than diffusion. Some of the results are found to have direct relevance to other physical problems, such as the light element depletion in sun-type stars. The large kurtosis found for downward moving particles at the base of the convection zone implies several extreme events.

Miesch, Mark↗

DOE OSTI2018

Data-Driven Wind Farm Optimization Incorporating Effects of Turbulence Intensity

We demonstrate assimilation of field data from a nacelle-mounted lidar and meteorological tower into a medium-fidelity Reynolds-Averaged Navier Stokes wind farm flow model to better predict the effects of atmospheric stability. Increased predictability under a variety of atmospheric conditions can lead to more effective control design and optimization of a wind farm. In particular, atmospheric stability affects wind turbine wake propagation and, therefore, aspects of wind farm control and performance, such as active wind farm control, layout optimization, and power output. Accurately modeling wakes in different stability conditions remains a persistent challenge. This paper presents an optimization framework that leverages high-fidelity field or simulation data to correct a lower-fidelity flow model. Optimal model corrections are found by solving a regularized, high-dimensional, gradient-based optimization problem using adjoint flowfield information. We validate the trained model against large eddy simulation results, and perform separate gradient-based layout optimizations of a simulated utility-scale wind farm to maximize power. Using the data-driven model corrections, we find that atmospheric stability significantly impacts layout optimization and power production: the optimal layout for stable conditions produced 9.1% more power than the optimal layout for unstable conditions, and the optimal layout for neutral conditions underperformed by 8.5% in unstable conditions.

17 WIND ENERGY↗

NASA NTRS2012

Time-Series Analyses of Supergranule Characteristics Compared Between SDO/HMI, SOHO/MDI and Simulated Datasets

Supergranulation is a well-observed solar phenomenon despite its underlying mechanisms remaining a mystery. Originally considered to arise due to convective motions, alternative mechanisms have been suggested such as the cumulative downdrafts of granules as well as displaying wave-like properties. Supergranule characteristics are well documented, however. Supergranule cells are approximately 35 Mm across, have lifetimes on the order of a day and have divergent horizontal velocities of around 300 mis, a factor of 10 higher than their central radial components. While they have been observed using Doppler methods for more than half a century, their existence is also observed in other datasets such as magneto grams and Ca II K images. These datasets clearly show the influence of supergranulation on solar magnetism and how the local field is organized by the flows of supergranule cells. The Heliospheric and Magnetic Imager (HMI) aboard the Solar Dynamics Observatory (SDO) continues to produce Doppler images enabling the continuation of supergranulation studies made with SOHO/MDI, but with superior temporal and spatial resolution. The size-distribution of divergent cellular flows observed on the photosphere now reaches down to granular scales, allowing contemporaneous comparisons between the two flow components. SOHO/MDI Doppler observations made during the minima of cycles 22/23 and 23/24 exhibit fluctuations of supergranule characteristics (global averages of the supergranule size, size-range and horizontal velocity) with periods of 3-5 days. Similar fluctuations have been observed in SDO/HMI Dopplergrams and the high correlation between co-temporal HMI & MOl suggest a solar origin. Their nature has been probed by invoking data simulations that produce realistic Dopplergrams based on MOl data.

Williams, Peter E.↗

NASA NTRS1981

The influence of autocorrelation in signature extraction: An example from a geobotanical investigation of Cotter Basin, Montana

The presence of positive serial correlation (autocorrelation) in remotely sensed data results in an underestimate of the variance-covariance matrix when calculated using contiguous pixels. This underestimate produces an inflation in F statistics. For a set of Thematic Mapper Simulator data (TMS), used to test the ability to discriminate a known geobotanical anomaly from its background, the inflation in F statistics related to serial correlation is between 7 and 70 times. This means that significance tests of means of the spectral bands initially appear to suggest that the anomalous site is very different in spectral reflectance and emittance from its background sites. However, this difference often disappears and is always dramatically reduced when compared to frequency distributions of test statistics produced by the comparison of simulated training sets possessing equal means, but which are composed of autocorrelated observations.

Labovitz, M. L.↗

NASA NTRS1982

The influence of autocorrelation in signature extraction - An example from a geobotanical investigation of Cotter Basin, MT

Labovitz, M. L.↗