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FY20 Verification of BISON Using Analytic and Manufactured Solutions
In 2010, the U.S. Department of Energy created its first Energy Innovation Hub, which is focused on developing high-fidelity and high-resolution Modeling and Simulation (M&S) tools for modeling of Light Water Reactors (LWRs). This hub, Consortium for Advanced Simulation of LWRs (CASL), has developed an LWR simulation tool called Virtual Environment for Reactor Applications (VERA). The multi-physics capability of VERA is achieved through the coupling of single-physics codes, including BISON, CTF, MPACT, and MAMBA. BISON is a fuel performance code which models the thermo-mechanical behavior of nuclear fuel using high performance M&S. It is capable of modeling traditional LWR fuel rods, fuel plates, and TRi-structural ISOtropic (TRISO) fuel particles. It can employ three-dimensional Cartesian, two-dimensional axisymmetric cylindrical, or one-dimensional radial spherical geometry. It includes empirical models for a large variety of fuel physics: temperature- and burnup-dependent thermal properties, fuel swelling and densification, fission gas production, cladding creep, fracture, cladding plasticity, and gap/plenum models. This document details a series of code verification test problems that are used to test BISON. These problems add confidence that the BISON code is a faithful representation of its underlying mathematical model. The suite of verification tests are mapped to the underlying conservation equations solved by the code: heat conduction, mechanics, and species conservation. Twenty-two problems are added for the heat conduction solution, two for the mechanics solution, and none for species conservation. Method of Manufactured Solutions (MMS) capability is demonstrated with three problems, and temperature drops across the fuel gap are tested.
Modeling Buried Object Brightness and Visibility for Ground Penetrating Radar
Comparing the observed brightness of various buried objects is a straightforward way to characterize the performance of a ground penetrating radar (GPR) system. However, a limitation arises. A simple comparison of buried object brightness values does not disentangle the effects of the GPR system itself from the system's operating environment and the objects being observed. Therefore, with brightness values exhibiting an unknown synthesis of systemic, environmental, and object factors, GPR system analysis becomes a convoluted affair. In this work, we use an experimentally collected dataset of over 25,000 object observations from five different multistatic radar arrays to develop models of buried object brightness and control for these various effects. Additionally, our modeling efforts provide a means for quantifying the relative brightness of GPR systems, the objects they detect, and the physical properties of those objects that influence observed brightness. To evaluate the models' performance on new object observations, we repeatedly simulate fitting them to half the dataset and predicting the observed brightness values of the unseen half. In addition, we introduce a method for estimating the probability that individual observations constitute a visible object, which aids in failure analysis, performance characterization, and dataset cleaning.
Modeling Partial Reflection Paths for Infrasound Analysis
Numerical methods enabling simulation of scattered and partially reflected infrasonic propagation paths produced by interaction with fine-scale structure in the middle atmosphere have been implemented in the infraGA ray tracing software. This capability enables simulation of ensonification in the classical stratospheric “shadow zone” that has been observed during the Humming Roadrunner and LSECE surface explosion campaigns as well as in other data sets. In the case of LSECE, a pair of stations roughly 140 kilometers east of the source location observed arrivals with celerities (horizontal group velocities) slightly slower than observed stratospheric paths at similar azimuths. The arrivals exhibited increasing trace velocity later in the wavetrain indicating a steepening of the arrival path for longer or slower propagation paths. Simulation of partially reflected paths using the updated infraGA software methods finds good agreement between observed and predicted infrasonic ensonification at these locations within the stratospheric shadow zone. Further development of the partial reflection physics and comparison with other data sets is needed to more robustly understand how such anomalous infrasonic signals can be predicted; however, the demonstration of this capability is a promising first step in such analyses.
Particle Sensitivity Analysis
We propose to develop a computational sensitivity analysis capability for Monte Carlo sampling-based particle simulation relevant to Aleph, Cheetah-MC, Empire, Emphasis, ITS, SPARTA, and LAMMPS codes. These software tools model plasmas, radiation transport, low-density fluids, and molecular motion. Our report demonstrates how adjoint optimization methods can be combined with Monte Carlo sampling-based adjoint particle simulation. Our goal is to develop a sensitivity analysis to drive robust design-based optimization for Monte Carlo sampling-based particle simulation - a currently unavailable capability.
Physics-informed machine learning of redox flow battery based on a two-dimensional unit cell model
In this paper, we present a physics-informed neural network (PINN) approach for predicting the performance of an all-vanadium redox flow battery, with its physics constraints enforced by a two-dimensional (2D) mathematical model. The 2D model, which includes 6 governing equations and 24 boundary conditions, provides a detailed representation of the electrochemical reactions, mass transport and hydrodynamics occurring inside the redox flow battery. To solve the 2D model with the PINN approach, a composite neural network is employed to approximate species concentration and potentials; the input and output are normalized according to prior knowledge of the battery system; the governing equations and boundary conditions are first scaled to an order of magnitude around 1, and then further balanced with a self-weighting method. Our numerical results show that the PINN is able to predict cell voltage correctly, but the prediction of potentials shows a constant-like shift. To fix the shift, the PINN is enhanced by further constrains derived from the current collector boundary. Finally, we show that the enhanced PINN can be even further improved if a small number of labeled data is available.
Dynamic Catalysis Fundamentals: I. Fast calculation of limit cycles in dynamic catalysis
Dynamic catalysis—the forced oscillation of catalytic reaction coordinate potential energy surfaces (PES)—has recently emerged as a promising method for the acceleration of heterogeneously-catalyzed reactions. Theoretical study of enhancement of rates and supra-equilibrium product yield via dynamic catalysis has, to-date, been severely limited by onerous computational demands of forward integration of stiff, coupled ordinary differential equations (ODEs) that are necessary to quantitatively describe periodic cycling between PESs. Here, we establish a new approach that reduces, by ≳108×, the computational cost of finding the time-averaged rate at dynamic steady state (i.e. the limit cycle for linear and nonlinear systems of kinetic equations). Our developments are motivated by and conceived from physical and mathematical insight drawn from examination of a simple, didactic case study for which closed-form solutions of rate enhancement are derived in explicit terms of periods of oscillation and elementary step rate constants. Generalization of such closed-form solutions to more complex catalytic systems is achieved by introducing a periodic boundary condition requiring the dynamic steady state solution to have the same periodicity as the kinetic oscillations and solving the corresponding differential equations by linear algebra or Newton-Raphson-based approaches. The methodology is well-suited to extension to non-linear systems for which we detail the potential for multiple solutions or solutions with different periodicities. For linear and non-linear systems alike, the acute decrement in computational expense enables rapid optimization of oscillation waveforms and, consequently, accelerates understanding of the key catalyst properties that enable maximization of reaction rates, conversions, and selectivities during dynamic catalysis.
Real-time spin systems from lattice field theory
We construct a lattice field theory method for computing the real-time dynamics of spin systems in a thermal bath. This is done by building on previous work of Takano with Schwinger-Keldysh and functional differentiation techniques. We derive a Schwinger-Keldysh path integral for generic spin Hamiltonians, then demonstrate the method on a simple system. Our path integral has a sign problem, which generally requires exponential run time in the system size, but requires only linear storage. The latter may place this method at an advantage over exact diagonalization, which is exponential in both. Our path integral is amenable to contour deformations, a technique for reducing sign problems.
Hybrid Particle Method for Computational Shock Physics
A long-standing area of research for Eulerian shock wave physics codes has been the treatment of strength and damage for materials. Here we present a method that will aid in the analysis of strength and failure in shock physics applications where excessive diffusion of critical variables can occur and control the solution outcome. Eulerian methods excel for large deformation simulations in general but are inaccurate in capturing structural behavior. Lagrangian methods provide better structural response, but finite element meshes can become tangled. Therefore, a technique for merging Lagrangian and Eulerian treatments of material response, within a single numerical framework, was implemented in the Multiple Component computational shock physics hydrocode. The capability is a Lagrangian/Eulerian Particle Method (LEPM) that uses particles to interface a Lagrangian treatment of material strength with a more traditional Eulerian treatment of the Equation of State (EOS). Lagrangian numerical methods avoid the advection diffusion found in Eulerian methods, which typically strongly affects strength constitutive law internal variables, such as equivalent plastic strain, porosity and/or damage. The Lagrangian capability enhances existing capabilities and permits accurate predictions of high rate, large deformation and/or shock of mechanical structures.
Essential Statistical Concepts
Statistical methods are an essential element to making quality measurements, allowing the organization and interrogation of data in a structured way. This introductory chapter describes key concepts of measurement statistics that are used in many nondestructive assay (NDA) methods and is intended as a primer to the reading list provided in the reference section. (Croft and Burr 2016; Smith 1991; Smith 2013; Taylor 1997; Triola 2017). The textbooks by Triola on elementary statistics (Figure 1), Taylor, and Smith (2013) introduce uncertainty analysis in the physical sciences. Smith (1991) provides a rigorous introduction with examples to correlated variables. These texts collectively offer an excellent foundation for understanding essential statistical concepts.
Update of the Nuclear Criticality Slide Rule Calculations: Plutonium systems – Delayed Fission Gamma
IRSN (France), LLNL (USA) and ORNL (USA) began a long-term collaboration effort in 2015 to update the nuclear criticality Slide Rule for the emergency response to a nuclear criticality accident. The Slide Rule permits the estimation of neutron and gamma dose rates and integrated doses based upon estimated fission yields, as a function of distance from the fission source, and time after criticality accidents for different critical systems. This paper presents results from the fourth phase of the current update of the Slide Rule project, in which delayed fission-product gamma (DFG) dose rates of unreflected plutonium critical systems were compared by several modern 3D radiation transport codes (MCNP, COG, SCALE), using updated flux-to-dose conversion factors. Dose rates are calculated for fissile material at five moderation ratios (H/Pu), at 1 m above the ground as a function of distance (between 30 cm and 1,200 m) from the external surface of the source to the center of the detector, and for periods between 1 s and 1,000 min after the critical instantaneous event. Further efforts have been devoted to the determination of the delayed gamma source, by comparing the time-dependent energy spectra obtained from several methods. Overall, DFG dose rates calculated by each participant led to consistent results. Extra effort is under way to identify the cause of the remaining differences, by comparing precisely the gamma source, and particularly nuclides inventories.
$\mathrm{CROPSR}$: an automated platform for complex genome-wide $\mathrm{CRISPR}$ g$\mathrm{RNA}$ design and validation
CRISPR/Cas9 technology has become an important tool to generate targeted, highly specific genome mutations. The technology has great potential for crop improvement, as crop genomes are tailored to optimize specific traits over generations of breeding. Many crops have highly complex and polyploid genomes, particularly those used for bioenergy or bioproducts. The majority of tools currently available for designing and evaluating gRNAs for CRISPR experiments were developed based on mammalian genomes that do not share the characteristics or design criteria for crop genomes. We have developed an open source tool for genome-wide design and evaluation of gRNA sequences for CRISPR experiments, CROPSR. The genome-wide approach provides a significant decrease in the time required to design a CRISPR experiment, including validation through PCR, at the expense of an overhead compute time required once per genome, at the first run. To better cater to the needs of crop geneticists, restrictions imposed by other packages on design and evaluation of gRNA sequences were lifted. A new machine learning model was developed to provide scores while avoiding situations in which the currently available tools sometimes failed to provide guides for repetitive, A/T-rich genomic regions. We show that our gRNA scoring model provides a significant increase in prediction accuracy over existing tools, even in non-crop genomes. CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments. CROPSR reduces the challenges of working in crops, and helps speed gRNA sequence design, evaluation and validation. We hope that the new software will accelerate discovery and reduce the number of failed experiments.
Safeguards-Informed Hybrid Imagery Dataset [Poster]
Deep Learning computer vision models require many thousands of properly labelled images for training, which is especially challenging for safeguards and nonproliferation, given that safeguards-relevant images are typically rare due to the sensitivity and limited availability of the technologies. Creating relevant images through real-world staging is costly and limiting in scope. Expert-labeling is expensive, time consuming, and error prone. We aim to develop a data set of both realworld and synthetic images that are relevant to the nuclear safeguards domain that can be used to support multiple data science research questions. In the process of developing this data, we aim to develop a novel workflow to validate synthetic images using machine learning explainability methods, testing among multiple computer vision algorithms, and iterative synthetic data rendering. We will deliver one million images – both real-world and synthetically rendered – of two types uranium storage and transportation containers with labelled ground truth and associated adversarial examples.
Combining data and theory for derivable scientific discovery with AI-Descartes
Abstract Scientists aim to discover meaningful formulae that accurately describe experimental data. Mathematical models of natural phenomena can be manually created from domain knowledge and fitted to data, or, in contrast, created automatically from large datasets with machine-learning algorithms. The problem of incorporating prior knowledge expressed as constraints on the functional form of a learned model has been studied before, while finding models that are consistent with prior knowledge expressed via general logical axioms is an open problem. We develop a method to enable principled derivations of models of natural phenomena from axiomatic knowledge and experimental data by combining logical reasoning with symbolic regression. We demonstrate these concepts for Kepler’s third law of planetary motion, Einstein’s relativistic time-dilation law, and Langmuir’s theory of adsorption. We show we can discover governing laws from few data points when logical reasoning is used to distinguish between candidate formulae having similar error on the data.
Multi-Fidelity Active Subspaces for Wind Farm Uncertainty Quantification
Wind plants operate in stochastic environments characterized by complex turbulent flow dynamics and high-dimensional random variables. A key step in uncertainty quantification studies is sensitivity analysis and dimension reduction that can facilitate the development of surrogate models to be used for forward and inverse propagation or optimization under uncertainty. Prior work has shown active subspaces are an effective tool for identifying important directions in the space of stochastic inputs; however, they have only been applied to single-fidelity wind plant models. In this study, we investigate the efficacy of a multi-fidelity active subspace method for analyzing the uncertainty in wind plant power output. The multi-fidelity active subspace estimator offers the promise of increased accuracy in identifying active subspaces as compared to a single-fidelity estimator for the same computational cost, or a reduction in cost for the same accuracy. This makes the study of uncertainty in larger wind plants and with higher fidelity physics tractable. The multi-fidelity active subspace method is applied to gridded and existing wind plant layouts with single and multiple inflow conditions and its performance for surrogate modeling and uncertainty propagation is compared against a single-fidelity active subspace method. This multi-fidelity approach yields substantial computational speedups of 2x - 3.4x across the test cases along with acceptable accuracy in surrogate modeling and computing statistical moments.
Materializing Inter-Channel Relationships With Multi-Density Woodcock Tracking
Volume rendering techniques for scientific visualization have recently shifted toward Monte Carlo (MC) methods for their flexibility and robustness, but their use in multi-channel visualization remains underexplored. Traditional multi-channel volume rendering often relies on arbitrary, non-physically based color blending functions that hinder interpretation. Here, we introduce multi-density Woodcock tracking, a simple extension of Woodcock tracking that leverages an MC method to produce high-fidelity, physically grounded multi-channel renderings without arbitrary blending. By generalizing Woodcock’s distance tracking, we provide a unified blending modality that also integrates blending functions from prior works. We further implement effects that enhance boundary and feature recognition. By accumulating frames in real-time, our approach delivers high-quality visualizations with perceptual benefits, demonstrated on diverse datasets.
Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome
This dataset contains the structural models for the primary transcripts of the Rhodospirillum rubrum proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. rubrum proteome to those available in the AlphaFold Protein Structure Database. For proteins that have been annotated as hypothetical, sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments. References AlphaFold v2 Multimer: https://doi.org/10.1101/2021.10.04.463034. References HHBlits: https://doi.org/10.1186/s12859-019-3019-7. References SAdLSA: https://doi.org/10.3389/fbinf.2021.689960.
Structural Models and Sequence Alignment Results of the Desulfovibrio vulgaris Proteome
This dataset contains the structural models for the primary transcripts of the Desulfovibrio vulgaris proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the D. vulgaris proteome to those available in the AlphaFold Protein Structure Database (AFDB). This is a bit more complicated since the proteins reporting in the AFDB originate from an outdated form of the D. vulgaris sequence. The different versions of the D. vulgaris gene annotation are collected in the Chronology subdirectory; further consideration of these changes on the structural space of the proteome are currently underway. For proteins that have been annotated as hypothetical, sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments. References AlphaFold v2 Multimer: https://doi.org/10.1101/2021.10.04.463034. References HHblits: hhtps://doi.org/10.1186/s12859-019-3019-7. References SAdLSA: hhtps://doi.org/10.3389/fbinf.2021.689960.