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DOE OSTI2015

Correlation functions from a unified variational principle: Trial Lie groups

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces the original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie–Poisson structure. At second order, the variational expression for two-time correlation functions separates–as does its exact counterpart–the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Abstract There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Evolving data standards for cryo-EM structures

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Explainable AI for Multivariate Time Series Pattern Exploration: Latent Space Visual Analytics With Temporal Fusion Transformer and Variational Autoencoders in Power Grid Event Diagnosis

Detecting and analyzing complex patterns in multivariate time-series data is crucial for decision-making in urban and environmental system operations. However, challenges arise from the high dimensionality, intricate complexity, and interconnected nature of complex patterns, which hinder the understanding of their underlying physical processes. Existing AI methods often face limitations in interpretability, computational efficiency, and scalability, reducing their applicability in real-world scenarios. This paper proposes a novel visual analytics framework that integrates two generative AI models, Temporal Fusion Transformer (TFT) and Variational Autoencoders (VAEs), to reduce complex patterns into lower-dimensional latent spaces and visualize them in 2D using dimensionality reduction techniques such as PCA, t-SNE, and UMAP with DBSCAN. These visualizations, presented through coordinated and interactive views and tailored glyphs, enable intuitive exploration of complex multivariate temporal patterns, identifying patterns’ similarities and uncover their potential correlations for a better interpretability of the AI outputs. The framework is demonstrated through a case study on power grid signal data, where it identifies multi-label grid event signatures, including faults and anomalies with diverse root causes. Additionally, novel metrics and visualizations are introduced to validate the models and assess the performance, efficiency, and consistency of latent maps generated by VAE, which have been utilized in prior studies for latent space cartography and used as a benchmark in this study, and the emerging TFT architecture under various configurations. These analyses provide actionable insights for model parameter tuning and reliability improvements. Comparative results highlight that TFT achieves shorter run times and superior scalability to diverse time-series data shapes compared to VAE. This work advances fault diagnosis in multivariate time series, fostering explainable AI to support critical system operations.

Explainable AI↗

DOE OSTI2025

Improved Guarantees for Optimal Nash Equilibrium Seeking and Bilevel Variational Inequalities

We consider a class of hierarchical variational inequality (VI) problems that subsumes VI-constrained optimization and several other problem classes, including the optimal solution selection problem and the optimal Nash equilibrium (NE) seeking problem. Our main contribution is threefold. (i) We consider bilevel VIs with monotone and Lipschitz continuous mappings and devise a single-timescale iteratively regularized extragradient method, named IR-EG 𝚖,𝚖 . We improve the existing iteration complexity results for addressing both bilevel VI and VI-constrained convex optimization problems. (ii) Under the strong monotonicity of the outer-level mapping, we develop a method named IR-EG 𝚜,𝚖 and derive faster guarantees than those in (i). We also study the iteration complexity of this method under a constant regularization parameter. These results appear to be new for both bilevel VIs and VI-constrained optimization. (iii) To our knowledge, complexity guarantees for computing the optimal NE in nonconvex settings do not exist. Motivated by this lacuna, we consider VI-constrained nonconvex optimization problems and devise an inexactly projected gradient method, named IPR-EG, where the projection onto the unknown set of equilibria is performed using IR-EG 𝚜,𝚖 with a prescribed termination criterion and an adaptive regularization parameter. We obtain new complexity guarantees in terms of a residual map and an infeasibility metric for computing a stationary point. Here, we validate the theoretical findings using preliminary numerical experiments for computing the best and the worst NEs.

bilevel optimization↗

DOE OSTI2017

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO 2 -spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

36 MATERIALS SCIENCE↗

DOE OSTI2022

CMB/kSZ and Compton-y Maps from 2500 deg 2 of SPT-SZ and Planck Survey Data

Abstract We present component-separated maps of the primary cosmic microwave background/kinematic Sunyaev–Zel’dovich (SZ) amplitude and the thermal SZ Compton- y parameter, created using data from the South Pole Telescope (SPT) and the Planck satellite. These maps, which cover the ∼2500 deg 2 of the southern sky imaged by the SPT-SZ survey, represent a significant improvement over previous such products available in this region by virtue of their higher angular resolution ( 1 .′ 25 for our highest-resolution Compton- y maps) and lower noise at small angular scales. In this work we detail the construction of these maps using linear combination techniques, including our method for limiting the correlation of our lowest-noise Compton- y map products with the cosmic infrared background. We perform a range of validation tests on these data products to test our sky modeling and combination algorithms, and we find good performance in all of these tests. Recognizing the potential utility of these data products for a wide range of astrophysical and cosmological analyses, including studies of the gas properties of galaxies, groups, and clusters, we make these products publicly available at http://pole.uchicago.edu/public/data/sptsz_ymap and on the NASA/LAMBDA website.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1982

Cartographic mapping study

The errors associated with planimetric mapping of the United States using satellite remote sensing techniques are analyzed. Assumptions concerning the state of the art achievable for satellite mapping systems and platforms in the 1995 time frame are made. An analysis of these performance parameters is made using an interactive cartographic satellite computer model, after first validating the model using LANDSAT 1 through 3 performance parameters. An investigation of current large scale (1:24,000) US National mapping techniques is made. Using the results of this investigation, and current national mapping accuracy standards, the 1995 satellite mapping system is evaluated for its ability to meet US mapping standards for planimetric and topographic mapping at scales of 1:24,000 and smaller.

Wilson, C.↗

NASA NTRS1986

Measurement of angular distribution of sound emission from training projectiles in subsonic flight

Training projectiles with nose ring cavities that produce intense whistles in stationary free-jet tests were shot in a relatively straight-line trajectory. A ground based microphone was used to obtain the angular distribution of sound intensity produced from the subsonically flying projectile. Data reduction required calculation of Doppler and attenuation factors which were determined based on a non-linear trajectory. Also, the directional sensitivity of the microphone was measured and used in the data reduction. Significant angular variation of sound intensity produced from the projectile was found which can be used to plot an intensity contour map on the ground. A full-scale field test confirmed the validity of the aeroacoustic concept of producing a relatively intense whistle from the projectile, and the usefulness of a real-time data acquisition system.

Cho, Y. I.↗

NASA NTRS1988

Measurement of sound emitted by flying projectiles with aeroacoustic sources

Training projectiles with axisymmetric ring cavities that produce intense tones in an airstream were shot in a straight-line trajectory. A ground-based microphone was used to obtain the angular distribution of sound intensity produced from the flying projectile. Data reduction required calculation of Doppler and attenuation factors. Also, the directional sensitivity of the ground-mounted microphone was measured and used in the data reduction. A rapid angular variation of sound intensity produced from the projectile was found that can be used to plot an intensity contour map on the ground. A full-scale field test confirmed the validity of the aeroacoustic concept of producing a relatively intense whistle from the projectile, and the usefulness of short-range flight tests that yield acoustic data free of uncertainties associated with diffraction, reflection, and refraction at jet boundaries in free-jet tests.

Cho, Y. I.↗

NASA NTRS1999

Generation of Level 3 SMMR and SSM/I Brightness Temperatures for the Period 1978-1999

The NOAA/NASA Pathfinder Program was initially designed to assure that certain key remote sensing data sets of particular significance to global change research were scientifically validated, consistently processed and made readily available to the research community at minimal cost. Through this Program the National Snow and Ice Data Center (NSIDC), University of Colorado has successfully processed, archived and distributed the Scanning Multichannel Microwave Radiometer (SMMR) and Special Sensor Microwave/Imager (SSM/I) Level 3 (EASE-Grid format) Pathfinder data sets for the period 1978 to 1999. These data are routinely distributed to approximately 150 researchers through various media including CD-ROM, 8 mm tape, ftp and the EOS Information Management System (IMS). At NSIDC these data are currently being applied in the development and validation of algorithms to derive snow water equivalent (NASA NAG5-6636), the mapping of frozen ground and the detection of the onset of melt over ice sheets, sea ice and snow cover. The EASE-Grid format, developed at NSIDC in conjunction with the SMMR-SSM/I Pathfinder project has also been applied to Advanced Very High Resolution Radiometer (AVHRR) and TOVS Pathfinder data, as well as ancillary data such as digital elevation, land cover classification and several in situ data sets. EASE-Grid will also be used for all land products derived from the NASA EOS AMSR-E instrument.

Partington, Kim↗

NASA NTRS2014

Current Pressure Transducer Application of Model-based Prognostics Using Steady State Conditions

Prognostics is the process of predicting a system's future states, health degradation/wear, and remaining useful life (RUL). This information plays an important role in preventing failure, reducing downtime, scheduling maintenance, and improving system utility. Prognostics relies heavily on wear estimation. In some components, the sensors used to estimate wear may not be fast enough to capture brief transient states that are indicative of wear. For this reason it is beneficial to be capable of detecting and estimating the extent of component wear using steady-state measurements. This paper details a method for estimating component wear using steady-state measurements, describes how this is used to predict future states, and presents a case study of a current/pressure (I/P) Transducer. I/P Transducer nominal and off-nominal behaviors are characterized using a physics-based model, and validated against expected and observed component behavior. This model is used to map observed steady-state responses to corresponding fault parameter values in the form of a lookup table. This method was chosen because of its fast, efficient nature, and its ability to be applied to both linear and non-linear systems. Using measurements of the steady state output, and the lookup table, wear is estimated. A regression is used to estimate the wear propagation parameter and characterize the damage progression function, which are used to predict future states and the remaining useful life of the system.

Fault Estimation↗

NASA NTRS2015

Convective Enhancement of Icing Roughness Elements in Stagnation Region Flows

To improve existing ice accretion simulation codes, more data regarding ice roughness and its effects on convective heat transfer are required. To build on existing research on this topic, this study used the Vertical Icing Studies Tunnel (VIST) at NASA Glenn Research to model realistic ice roughness in the stagnation region of a NACA 0012 airfoil. Using the VIST, a test plate representing the leading 2% chord of the airfoil was subjected to flows of 7.62 m/s (25 ft/s), 12.19 m/s (40 ft/s), and 16.76 m/s (55 ft/s). The test plate was fitted with 3 surfaces, each with a different representation of ice roughness: 1) a control surface with no ice roughness, 2) a surface with ice roughness with element height scaled by 10x and streamwise rough zone width from the stagnation point scaled by 10x, and 3) a surface with ice roughness with element height scaled by 10x and streamwise rough zone width from the stagnation point scaled by 25x. Temperature data from the tests were recorded using an infrared camera and thermocouples imbedded in the test plate. From the temperature data, a convective heat transfer coefficient map was created for each case. Additional testing was also performed to validate the VIST's flow quality. These tests included five-hole probe and hot-wire probe velocity traces to provide flow visualization and to study boundary layer formation on the various test surfaces. The knowledge gained during the experiments will help improve ice accretion codes by providing heat transfer coefficient validation data and by providing flow visualization data helping understand current and future experiments performed in the VIST.

Icing↗

NASA NTRS2017

Modeling a Packed Bed Reactor Utilizing the Sabatier Process

A numerical model is being developed using Python which characterizes the conversion and temperature profiles of a packed bed reactor (PBR) that utilizes the Sabatier process; the reaction produces methane and water from carbon dioxide and hydrogen. While the specific kinetics of the Sabatier reaction on the RuAl2O3 catalyst pellets are unknown, an empirical reaction rate equation1 is used for the overall reaction. As this reaction is highly exothermic, proper thermal control is of the utmost importance to ensure maximum conversion and to avoid reactor runaway. It is therefore necessary to determine what wall temperature profile will ensure safe and efficient operation of the reactor. This wall temperature will be maintained by active thermal controls on the outer surface of the reactor. Two cylindrical PBRs are currently being tested experimentally and will be used for validation of the Python model. They are similar in design except one of them is larger and incorporates a preheat loop by feeding the reactant gas through a pipe along the center of the catalyst bed. The further complexity of adding a preheat pipe to the model to mimic the larger reactor is yet to be implemented and validated; preliminary validation is done using the smaller PBR with no reactant preheating. When mapping experimental values of the wall temperature from the smaller PBR into the Python model, a good approximation of the total conversion and temperature profile has been achieved. A separate CFD model incorporates more complex three-dimensional effects by including the solid catalyst pellets within the domain. The goal is to improve the Python model to the point where the results of other reactor geometry can be reasonably predicted relatively quickly when compared to the much more computationally expensive CFD approach. Once a reactor size is narrowed down using the Python approach, CFD will be used to generate a more thorough prediction of the reactors performance.

Reactor↗

NASA NTRS2020

Wildfire Smoke Particle Properties and Evolution, From Space-Based Multi-Angle Imaging II: The Williams Flats Fire during the FIREX-AQ Campaign

Although the characteristics of biomass burning events and the ambient ecosystem determine emitted smoke composition, the conditions that modulate the partitioning of black carbon (BC) and brown carbon (BrC) formation are not well understood, nor are the spatial or temporal frequency of factors driving smoke particle evolution, such as hydration, coagulation, and oxidation, all of which impact smoke radiative forcing. In situ data from surface observation sites and aircraft field campaigns offer deep insight into the optical, chemical, and microphysical traits of biomass burning (BB) smoke aerosols, such as single scattering albedo (SSA) and size distribution, but cannot by themselves provide robust statistical characterization of both emitted and evolved particles. Data from the NASA Earth Observing System’s Multi-Angle Imaging SpectroRadiometer (MISR) instrument can provide at least a partial picture of BB particle properties and their evolution downwind, once properly validated. Here we use in situ data from the joint NOAA/NASA 2019 Fire Influence on Regional to Global Environments Experiment-Air Quality (FIREX-AQ) field campaign to assess the strengths and limitations of MISR-derived constraints on particle size, shape, light-absorption, and its spectral slope, as well as plume height and associated wind vectors. Based on the satellite observations, we also offer inferences about aging mechanisms effecting downwind particle evolution, such as gravitational settling, oxidation, secondary particle formation, and the combination of particle aggregation and condensational growth. This work builds upon our previous study, adding confidence to our interpretation of the remote-sensing data based on an expanded suite of in situ measurements for validation. The satellite and in situ measurements offer similar characterizations of particle property evolution as a function of smoke age for the 06 August Williams Flats Fire, and most of the key differences in particle size and absorption can be attributed to differences in sampling and changes in the plume geometry between sampling times. Whereas the aircraft data provide validation for the MISR retrievals, the satellite data offer a spatially continuous mapping of particle properties over the plume, which helps identify trends in particle property downwind evolution that are ambiguous in the sparsely sampled aircraft transects. The MISR data record is more than two decades long, offering future opportunities to study regional wildfire plume behavior statistically, where aircraft data are limited or entirely lacking.

biomass burning↗

NASA NTRSDate not supplied

Surface Instability of Liquid Propellants in Microgravity During Pulsed Settling Operations

Pulsing reaction control system (RCS) thrusters, vent valves, or other propulsion devices can preserve propellant resources in space, but this operation also effectively introduces a vibration to the vehicle. When the vibration is perpendicular to the liquid propellant surface, Faraday waves may be generated at the liquid-vapor interface. These Faraday instabilities can perturb or break up the liquid surface of cryogenic tanks, leading to inefficiencies in thermal management or even ullage collapse. Drawing from theory and experiments, an engineering model defining the allowable design regions for pulsed settling in microgravity was assembled and verified with computational fluid dynamics (CFD) simulations. A traditional settling metric, the Bond number, was also overlaid in the model to indicate which duty cycles were insufficient to overcome surface tension and aggregate propellant. Mission planners and engineers can consult the tool to rapidly evaluate the stability of a liquid-vapor interface given the pulse frequency and the excitation acceleration. Expressions developed for Faraday waves induced by a sinusoidal forcing input at standard gravity were found to provide excellent predictive capabilities for pulsed, or rectangular, waveforms in the absence of a consistent gravitational acceleration. This study extends the usage of these equations to an alternative forcing function and microgravity environments for the purpose of estimating natural frequencies, surface mode shapes, surface wave amplitudes, and the onset of droplet ejection. CFD simulations with the Loci/STREAM-VoF (Volume of Fluid) solver were initially validated against experimental results in standard gravity. Discrete points on the design map were then investigated with CFD and confirmed that the engineering model reliably indicates surface stability and most Faraday wave characteristics without requiring higher-fidelity tools. The engineering model is highly extensible and can be adapted for various propellant fill fractions, fluid properties, and tank sizes.

Faraday Waves↗

NASA NTRSDate not supplied

Surface Instability of Liquid Propellants in Microgravity During Pulsed Settling Operations

Faraday Waves↗