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DOE OSTI2021

Gradient-based optimization of 3D MHD equilibria

Using recently developed adjoint methods for computing the shape derivatives of functions that depend on magnetohydrodynamic (MHD) equilibria (Antonsen et al. , J. Plasma Phys. , vol. 85, issue 2, 2019; Paul et al. , J. Plasma Phys. , vol. 86, issue 1, 2020), we present the first example of analytic gradient-based optimization of fixed-boundary stellarator equilibria. We take advantage of gradient information to optimize figures of merit of relevance for stellarator design, including the rotational transform, magnetic well and quasi-symmetry near the axis. With the application of the adjoint method, we reduce the number of equilibrium evaluations by the dimension of the optimization space ( ${\sim }50\text {--}500$ ) in comparison with a finite-difference gradient-based method. We discuss regularization objectives of relevance for fixed-boundary optimization, including a novel method that prevents self-intersection of the plasma boundary. We present several optimized equilibria, including a vacuum field with very low magnetic shear throughout the volume.

Physics↗

DOE OSTI2019

Estimation of Melting-Layer Cooling Rate from Dual-Polarization Radar: Spectral Bin Model Simulations

Diabatic cooling from hydrometeor phase changes in the stratiform melting layer is of great interest to both operational forecasters and modelers for its societal and dynamical consequences. Attempts to estimate the melting-layer cooling rate typically rely on either the budgeting of hydrometeor content estimated from reflectivity Z or model-generated lookup tables scaled by the magnitude of Z in the bright band. Recent advances have been made in developing methods to observe the unique polarimetric characteristics of melting snow and the additional microphysical information they may contain. However, to date no work has looked at the thermodynamic information available from the polarimetric radar brightband signature. In this study, a one-dimensional spectral bin model of melting snow and a coupled polarimetric operator are used to study the relation between the polarimetric radar bright band and the melting-layer cooling rate. Simulations using a fixed particle size distribution (PSD) and variable environmental conditions show that the height and thickness of the bright band and the maximum brightband Z and specific differential phase shift [Formula: see text] are all sensitive to the ambient environment, while the differential reflectivity [Formula: see text] is relatively insensitive. Additional simulations of 2700 PSDs based on in situ observations above the melting layer indicate that the maximum Z, [Formula: see text], and [Formula: see text] within the melting layer are poorly correlated with the maximum cooling rate while [Formula: see text] is strongly correlated. Finally, model simulations suggest that, in addition to riming, concurrent changes in aggregation and precipitation intensity and the associated cooling may plausibly cause observed sagging brightband signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Force-Modulated Selectivity of the Rhodium-Catalyzed Hydroformylation of 1-Alkenes

Here we quantify the regio- chemo-, and enantioselectivity of the hydroformylation of 1-alkenes catalyzed by Rh(I) complexes containing chiral macrocyclic biaryl bis(phosphine) ligands as a function of mechanical force applied to the biaryl backbone of these ligands. Extension forces increase the regioselectivity of the hydroformylation of 1-octene from l:b = 1.2 to 1.9 and decrease the chemoselectivity for C 9 aldehyde relative to 2-octene from 96% to 20% across a ~230 pN change in applied force. Extension forces decrease the enantioselectivity of the hydroformylation of styrene from 28% to 18% ee across a similar force range. Variable temperature 1 H and 31 P NMR analysis of five-coordinate rhodium complexes of the form (P–P)Rh(CO) 2 H established structures in which the bisphosphine ligand occupies one equatorial and one apical position in the trigonal bipyramid with rapid interconversion of the equatorial and apical phosphorus atoms ($ΔG^‡_{223 \text{K}}$ = 9.6–9.9 kcal/mol). Neither the isomeric composition nor fluxional behavior of these complexes was detectably perturbed across a ~300 pN change in applied force.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Complete collision data set for electrons scattering on molecular hydrogen and its isotopologues: I. Fully vibrationally-resolved electronic excitation of H 2 $X^1Σ^+_g)$

Here, we present a comprehensive set of vibrationally-resolved cross sections for electron-impact electronic excitation of molecular hydrogen suitable for implementation in collisional-radiative models. The adiabatic-nuclei molecular convergent close-coupling method is used to calculate cross sections for excitation of all bound vibrational levels and dissociative excitation of the B 1 Σ u + , C 1 Π u , E F 1 Σ g + , B ′ 1 Σ u + , G K 1 Σ g + , I 1 Π g , J 1 Δ g , D 1 Π u , H 1 Σ g + , b 3 Σ u + , c 3 Π u , a 3 Σ g + , e 3 Σ u + , d 3 Π u , h 3 Σ g + , g 3 Σ g + , i 3 Π g , and j 3 Δ g electronic states from all –14 bound vibrational levels of the ground electronic ($\text{X}$ $^1&#x3A3^+_g$) state. The data set consists of cross sections from threshold to 500 eV for over 5000 transitions, representing all possible electronic and vibrational transitions between the state and the –3 singlet and triplet states (where refers to the united-atoms-limit principle quantum number). The cross sections are presented in graphical form and provided as both numerical values and analytic fit functions in supplementary data files.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2017

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗

DOE OSTI2022

Stochastic Neutronics Primer (Volume I)

The purpose of this document is to introduce the elementary concepts and to build a concrete understanding of the stochastic theory of neutron transport to the motivated undergraduate student, the Ph.D. engineer/physicist/mathematician, and the staff scientist or professor learning yet another new skill. The authors understand that there are many learning types- from visual to analytical to repetitive to word-based to analogy-based (and combinations thereof)- and so we have tasked ourselves with providing as many representations as possible within to ensure every reader a fruitful endeavor. This document is written as a set of chapters that continually build upon the previous chapter. In this chapter, we provide the discussion, motivation, and background topics for the remainder of the text.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

Chain, Patrick↗

DOE OSTI2023

Natural Language Processing for Text Based Event Extraction: Identifying Events of Interest Related to Worldwide State-Sponsored Civil Nuclear Power

Beginning in FY20, SRNL was funded by the National Nuclear Security Administration’s Office of Defense Nuclear Non-Proliferation Research and Development to develop a prototype natural language processing/natural language understating machine learning-based modeling and analysis pipeline to extract and forecast events of interest from massive open data sources. The working hypothesis within the approach is that contextual shifts in key words and phrases act as indicators of events of interest over time. Therefore, by identifying points in time where contextual shifts occur, events of interest can be extracted along with explicit and implicit connections of entities and activities. The development of the preliminary prototype pipeline proved successful, meriting further testing of the pipeline on more broad topical domains and in a worldwide data environment. Therefore, SRNL, in collaboration with the Sanghani Center for Artificial Intelligence and Data Analytics at Virginia Tech, have continued development with a test case of identifying events of interest related to worldwide state-sponsored civil nuclear power in open data sources. In the first year of this follow-on effort, the team has curated domain-specific data corpuses using an automated scheme and applied the modeling and analysis pipeline. This robust, focused, and efficient approach consists of an ensemble of analyses applied to time dependent word embedding models that are trained on the data corpuses. In this report, the team has demonstrated the capability of the existing pipeline (as development has continued in parallel) by exploring several specific case-studies centered around Rosatom’s international activities regarding the planning, construction, operation, and/or shutdown of nuclear reactors. A basic timeline events has been generated by manually cataloging known “milestone” events that have occurred at reactors in Turkey, Finland, Hungary, and Egypt and compared with the output of the modeling pipeline. In this approach, the team has characterized the lead time using the prototype pipeline, as well as the ability to capture relevant information, which proved 100% successful. A deep dive example of the Akkuyu reactor (Turkey) is presented that shows the breadth of information that can be captured using the approach. In this case study, events were extracted pertaining to the planning/construction of Akkuyu including protests from the population, information campaigns in response to the protests, forged regulatory documents and lawsuits, budgetary/shareholder information, geopolitical tensions, and the various construction milestones. This has demonstrated the pipeline’s utility as a research aid or real-time event extraction tool, where summary-level information and detailed text extractions from millions of articles or Tweets across long time periods can be generated with significantly less effort than current techniques.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Gamma-ray Exportable Adjustable Spectrum Evolution

An initial number of fissions on a fissile/fissionable material, defined by ENDF library availability, is used to produce an initial inventory of fission products (FPs). The FPs are decayed using full, analytical solutions to the Bateman equations to calculate the FP inventory at a user-specified time. The radiation detector, a high-purity germanium (HPGe) detector, has been modeled using every gamma-ray in the ENDF/TENDL libraries individually, and the modeled response can be multiplied by the activity of each fission product to determine a full, energy dependent detector response, including dead time. The detector response can be output as a PeakEasy (.spe) file, or as a text file. Since each radioisotope's inventory is known, the proportion to the total may be shown for each isotope, as well as many radionuclides in a user-specified energy window. Full execution and display of results takes 1-3 seconds, depending on the complexity of the input parameters.

Holschuh, ThomasV [Idaho National Laboratory (INL)↗

DOE OSTI2020

Interactive Visualizations for Communicating Compliance and Sustainability Statements in Annual Site Environmental Reports - 20419

The annual reports of organizations are a recurring type of public disclosure that communicates what an organization has done and/or plans to do. Worldwide, organizations use annual reports as powerful instruments for communication that is rich in narrative content and visuals. From the perspective of the leadership of an organization, statutory annual reports are communication devices to stakeholders. By analogy, from the perspective of stakeholders, the annual reports are learning devices that presents stakeholders with contents to generate knowledge about an organization. We have chosen the online accessible U.S. Department of Energy (DOE) Annual Site Environmental Reports (ASERs) as a collection of resources for communicating and learning the environmental management strategies on environmental compliance and environmental sustainability. Environmental Compliance 'consists of regulatory compliance and monitoring programs that implement federal, state, and local requirements, agreements, and permits.' Environmental Sustainability 'promotes and integrates initiatives such as energy and natural resource conservation, waste minimization, green remediation, and the use of sustainable products and services.' Interactive visualizations of textual data designed with visual analytics software can allow stakeholders to interact with statements on the environmental management strategies by performing diverse actions that promote learning. These actions include annotating, comparing, filtering, navigating, selecting and sharing relevant statements. We expect that the possibility of these multiple actions in an interactive manner help stakeholders to learn more effectively about the environmental strategies at U.S. DOE sites. The current case study for the project is a collection of 1,894 annotated (value-added) statements (sentence text) from the eight chapters of the 2017 Savanah River Site (SRS) annual site environmental report. The preliminary interactive visualizations are available online. (authors)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

The Bloch equation for spin dynamics in electron storage rings: Computational and theoretical aspects

In this paper, we describe our work on spin polarization in high-energy electron storage rings which we base on the Full Bloch equation (FBE) for the polarization density and which aims towards the [Formula: see text] option of the proposed Future Circular Collider (FCC-ee) and the proposed Circular Electron Positron Collider (CEPC). The FBE takes into account non spin-flip and spin-flip effects due to synchrotron radiation including the spin-diffusion effects and the Sokolov–Ternov effect with its Baier–Katkov generalization as well as the kinetic-polarization effect. This mathematical model is an alternative to the standard mathematical model based on the Derbenev–Kondratenko formulas. For our numerical and analytical studies of the FBE, we develop an approximation to the latter to obtain an effective FBE. This is accomplished by finding a third mathematical model based on a system of stochastic differential equations (SDEs) underlying the FBE and by approximating that system via the method of averaging from perturbative ODE theory. We also give an overview of our algorithm for numerically integrating the effective FBE. This discretizes the phase space using spectral methods and discretizes time via the additive Runge–Kutta (ARK) method which is a high-order semi-implicit method. We also discuss the relevance of the third mathematical model for spin tracking.

Physics↗

DOE OSTI2024

A reactive electrochemomechanical theory for growth and remodeling of polyelectrolyte hydrogels and application to dynamic polymerization of $\text{DNA}$ hydrogels

Here this study develops a framework for growth and remodeling of active polyelectrolyte hydrogels that accounts for effects of compositional changes on the mechanical response. By developing a reactive electrochemomechanical theory, thermodynamical constraints upon reactive and remodeling processes are elucidated within a general framework that allows any number of chemical reactions to evolve the response of the gel and transfer mass and charge between constituents. Fully coupled, nonlinear constitutive relations are adopted for molar fluxes, allowing exploration of effects including cross-diffusion, electrophoresis, and electro-osmosis. A robust finite element implementation is developed in the open source FEBio software (febio.org) by exploiting an equivalence between electrochemomechanics and mixture theory. The implementation is verified against analytical solutions for free swelling, and a proper reduction to a prior chemomechanical theory is demonstrated for neutral gels swollen only by a solvent with no solutes. The theory and implementation are then applied to model the tunable large swelling achieved through dynamic polymerization of DNA crosslinkers seen in our recently developed experimental hydrogel system (Cangialosi et al., 2017). A novel constitutive model for reaction-driven evolution of the locking stretch λ L in a non-Gaussian mechanical free energy was developed, where the increasing concentration of DNA crosslinkers makes further swelling energetically favorable. With a single free parameter, excellent agreement was found between measured and predicted equilibrium swelling ratios. This study demonstrated the ability to extend the electrochemomechanical framework to include chemical reactions and composition-aware constitutive models, and showed that development of reactive models allows simulation of complex dynamic polymerization phenomena not treated before. The theoretical frame here can be further expanded in scope to incorporate additional non-ideal and nonlinear phenomena.

42 ENGINEERING↗

DOE OSTI2024

Understanding Event Trajectories Across Massive Temporal Datasets with Word Embeddings and Visualization

In collaboration with researchers from Virginia Tech, Savannah River National Laboratory has continued development of a natural language processing pipeline to identify and extract events of interest from massive open data sources in the domain of worldwide state-sponsored civil nuclear energy. The foundation of the pipeline is built on compass aligned temporal word embedding models, whereby contextual shifts are automatically identified by comparing keyword embedding vectors across successive time windows. Within the approach, a contextual shift indicates the occurrence of a potential event of interest. However, in such a broad topical domain that captures events at a global scale, across various life cycle stages, and across numerous different technology types, a user that is monitoring events may have broad interests in capturing many different event types with varying degrees of signal. As such, the quantity of information that may be returned from an automated event extraction pipeline can be substantial, requiring manual effort to sift through the information to identify any relevant bits of information. Therefore, a more streamlined workflow that aids in directing a user toward specific information at different points in time is necessary. The workflow presented here has been developed with this concept in mind, built on top of the initial prototype event extraction pipeline, whereby a user can analyze temporal text-based data sources at multiple different contextual levels to isolate key points in time and key subdomains captured within a data corpus. Using multiple corpuses that consist of approximately 7 million Tweets and 7 million news articles, the team has extended compass aligned temporal word embedding models to establish an interconnected and hierarchical structure that relates known key words of interest to documents, local topics (i.e., within a time window), and global topics across the corpuses. All of this information is packaged into a visual analytics system that is linked to the information extraction pipeline and enables a user to identify contextual information that describes the evolution of a high dimensional embedding space across time to isolate changes of interest and explore associated events. This report demonstrates the use of these analytics and a means to fuse information across multiple datasets.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Water narratives in local newspapers within the United States

Sustainable use of water resources continues to be a challenge across the globe. This is in part due to the complex set of physical and social behaviors that interact to influence water management from local to global scales. Analyses of water resources have been conducted using a variety of techniques, including qualitative evaluations of media narratives. This study aims to augment these methods by leveraging computational and quantitative techniques from the social sciences focused on text analyses. Specifically, we use natural language processing methods to investigate a large corpus (approx. 1.8M) of newspaper articles spanning approximately 35 years (1982–2017) for insights into human-nature interactions with water. Focusing on local and regional United States publications, our analysis demonstrates important dynamics in water-related dialogue about drinking water and pollution to other critical infrastructures, such as energy, across different parts of the country. Our assessment, which looks at water as a system, also highlights key actors and sentiments surrounding water. Extending these analytical methods could help us further improve our understanding of the complex roles of water in current society that should be considered in emerging activities to mitigate and respond to resource conflicts and climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Historic climate, cosmogenic 10Be, denudation-rate, and geospatial datasets from the Pikes Peak region, Colorado, USA

This data package contains geographic information system (GIS) layers and tabular datasets associated with the study of elevation-dependent denudation rates on Pikes Peak in the Front Range of the Rocky Mountains, Colorado, USA. The package includes GIS layers used to produce the study-area map, including sample locations, sample watershed boundaries, the Pikes Peak batholith, Pleistocene glacier extent, weather station locations, and elevation and hillshade rasters, together with comma-separated value (CSV) tables and matching CSV data dictionaries. These mapped layers provide the geographic framework for interpreting denudation patterns across the Pikes Peak region and for relating sample locations to watershed geometry, bedrock setting, glacial history, and nearby climate stations. The first group of tables reports climate and geospatial context for the study area. These files include station-based temperature and precipitation data used to characterize elevational gradients in mean annual climate and monthly climate seasonality, sample locations, denudation-rate and topographic metrics, fixed frost-cracking model parameters, frost-cracking intensity and precipitation-frequency metrics, and stream-power inversion results. Together, these data provide the basis for evaluating how denudation varies with elevation, climate, and landscape form across sampled catchments on Pikes Peak. The second group of tables reports cosmogenic nuclide and erosion-model results used in the denudation analysis. Included files contain accelerator mass spectrometry (AMS) measurements for in situ-produced cosmogenic beryllium-10 (10Be), including sample identifiers, measured 10Be:9Be ratios, analytical uncertainties, carrier mass, quartz mass, blank corrections, blank-group statistics, and calculated 10Be concentrations and uncertainties. Additional tables summarize stream-power-law inversion results for sampled catchments, including optimized model parameters, predicted erosion rates, residual metrics, channel-pixel counts, and convergence status, as well as regression equations and summary statistics used to evaluate relationships among elevation, climate, frost cracking, precipitation forcing, and denudation rate. The package contains GIS files, comma-separated value files (.csv), Microsoft Excel files (.xlsx), CSV data dictionaries, a file-level metadata table, and a readme text file.

10Be cosmogenic nuclides↗

DOE OSTI2020

Effective theory of superconductivity in strongly coupled amorphous materials

A theory of phonon-mediated superconductivity in strong-coupling amorphous materials is developed based on an effective description of structural disorder and its effect on the vibrational spectrum. The theory accounts for the diffusivelike transport of vibrational excitations due to disorder-induced scattering within the Eliashberg theory of strong-coupling superconductivity. The theory provides a good analytical description of the Eliashberg function $α^2F(ω)$ in comparison with experiments and allows one to disentangle the effects of transverse and longitudinal excitations on the Eliashberg function. In particular, it shows that the transverse excitations play a crucial role in driving an increase or excess in the Eliashberg function at low energy, which is related to the boson peak phenomenon in vibrational spectra of glasses. This low-energy excess, on the one hand, drives an enhancement of the electron-phonon coupling but at the same time reduces the characteristic energy scale $ω_{\text{log}}$ in the Allen-Dynes formula. As a consequence, the nonmonotonicity of $T_c$ as a function of alloying (disorder) in Pb-based systems can be rationalized. Further, the case of Al-based systems, where disorder increases $T_c$ from the start, is also analyzed. General material-design principles for enhancing $T_c$ in amorphous superconductors are presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Comment on “Additional Insights Between Fermi-Löwdin Orbital SIC and the Localization Equation Constraints in SIC-DFT”

In a recent Letter, Aquino and Wong (AW) analyze the connection between the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) and the traditional Perdew– Zunger self-interaction correction (PZ-SIC) methods. In this work, the authors present a derivation of the conditions required to minimize the SIC density functional theory (DFT) total energy in FLO-SIC. These involve the gradient of the energy with respect to parameters known as Fermi-orbital descriptors (FODs) (called orbital “centroids” in ref 1) that are used together with the total charge density to determine the Fermi- Löwdin orbitals (FLOs). AW state that the conditions, the vanishing of the FOD gradient components, “resemble” the localization equations (LE), the minimum energy conditions in traditional PZ-SIC. The LE involve the equality of certain off-diagonal matrix elements of different orbital-dependent Hamiltonians. While AW are careful to say that their equations do not prove the mathematical equivalence of the two methods, the discussion in the text and the graphical table of contents figure suggest that vanishing FOD gradients imply satisfaction of the LE and vice versa, and hence that the methods are equivalent. We believe this ambiguity clouds an important issue, rather than clarifying it.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Lightweight and effective tensor sensitivity for atomistic neural networks

Atomistic machine learning focuses on the creation of models that obey fundamental symmetries of atomistic configurations, such as permutation, translation, and rotation invariances. In many of these schemes, translation and rotation invariance are achieved by building on scalar invariants, e.g., distances between atom pairs. There is growing interest in molecular representations that work internally with higher rank rotational tensors, e.g., vector displacements between atoms, and tensor products thereof. Here, we present a framework for extending the Hierarchically Interacting Particle Neural Network (HIP-NN) with Tensor Sensitivity information (HIP-NN-TS) from each local atomic environment. Crucially, the method employs a weight tying strategy that allows direct incorporation of many-body information while adding very few model parameters. We show that HIP-NN-TS is more accurate than HIP-NN, with negligible increase in parameter count, for several datasets and network sizes. As the dataset becomes more complex, tensor sensitivities provide greater improvements to model accuracy. In particular, HIP-NN-TS achieves a record mean absolute error of 0.927 $\frac{\text{kcal}}{\text{mol}}$ for conformational energy variation on the challenging COMP6 benchmark, which includes a broad set of organic molecules. We also compare the computational performance of HIP-NN-TS to HIP-NN and other models in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗