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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Dynamic time-warping correction for shifts in ultrahigh resolving power ion mobility spectrometry and structures for lossless ion manipulations

Detection of arrival time shifts between ion mobility spectrometry (IMS) separations can limit achievable resolving power (Rp), particularly when multiple separations are summed or averaged, as commonly practiced. Such variations are more apparent in higher Rp measurements, and are particularly evident in long path length traveling wave structures for lossless ion manipulations (SLIM) IMS due to their typically much longer separation times. Here we explore the utility of a data processing approaches employing linear alignment (LA) and nonlinear dynamic time warping (DTW) of IMS separations to correct for variations between separations, such as due to pressure fluctuations. For multipass SLIM IMS separations, where narrow mobility range measurements have arrival times that can extend to several seconds, the LA approach effectively corrected for such variations, and significantly improvement Rp for summed separations. However, LA was much less effective for high Rp broad mobility range separations, such as obtained with multilevel SLIM IMS. Changes in IMS arrival times ions were observed to be correlated with small pressure changes, with approximately 0.6% relative arrival time shifts being common, sufficient to result in a loss of Rp for summed separations. Comparison of the approaches showed DTW alignment performed similarly to LA when used over a narrow mobility range, but was significantly better (providing narrower peaks and higher signal intensities) for wide mobility range data. We found the DTW approach increased Rp by as much as 115% for measurements in which 50 IMS separations over 2 seconds were summed, and leading to a large improvement in effective Rp. We conclude that DTW is superior to LA for ultrahigh resolution broad mobility range SLIM IMS separations, correcting for ion arrival time shifts regardless of the cause. Our tool is publicly available for use with universal ion mobility format (.UIMF) and text (.txt) files.

Data alignment, dynamic time warping, ion mobility↗
DOE OSTI2025

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Abstract Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Mathivanan, Ramesh Kanna↗
DOE OSTI2023

A Novel Spatial-Temporal Variational Quantum Circuit to Enable Deep Learning on NISQ Devices

Quantum computing presents a promising approach for machine learning with its capability for extremely parallel computation in high-dimension through superposition and entanglement. Despite its potential, existing quantum learning algorithms, such as Variational Quantum Circuits (VQCs), face challenges in handling more complex datasets, particularly those that are not linearly separable. What’s more, it encounters the deployability issue, making the learning models suffer a drastic accuracy drop after deploying them to the actual quantum devices. To overcome these limitations, this paper proposes a novel spatial-temporal design, namely “ST-VQC”, to integrate nonlinearity in quantum learning and improve the robustness of the learning model to noise. Specifically, ST-VQC can extract spatial features via a novel block-based encoding quantum sub-circuit coupled with a layer-wise computation quantum sub-circuit to enable temporal-wise deep learning. Additionally, a SWAP-Free physical circuit design is devised to improve robustness. These designs bring a number of hyperparameters. After a systematic analysis of the design space for each design component, an automated optimization framework is proposed to generate the ST-VQC quantum circuit. The proposed ST-VQC has been evaluated on two IBM quantum processors, ibm-cairo with 27 qubits and ibmq-lima with 7 qubits to assess its effectiveness. The results of the evaluation on the standard dataset for binary classification show that ST-VQC can achieve over 30% accuracy improvement compared with existing VQCs on actual quantum computers. Moreover, on a non-linear synthetic dataset, the STVQC outperforms a linear classifier by 27.9%, while the linear classifier using classical computing outperforms the existing VQC by 15.58%.

Li, Jinyang↗
DOE OSTI2025

Full event particle-level unfolding with variable-length latent variational diffusion

The measurements performed by particle physics experiments must account for the imperfect response of the detectors used to observe the interactions. One approach, unfolding, statistically adjusts the experimental data for detector effects. Recently, generative machine learning models have shown promise for performing unbinned unfolding in a high number of dimensions. However, all current generative approaches are limited to unfolding a fixed set of observables, making them unable to perform full-event unfolding in the variable dimensional environment of collider data. A novel modification to the variational latent diffusion model (VLD) approach to generative unfolding is presented, which allows for unfolding of high- and variable-dimensional feature spaces. The performance of this method is evaluated in the context of semi-leptonic t\bar{t} t t ‾ production at the Large Hadron Collider.

Shmakov, Alexander↗
DOE OSTI2025

A Game-Theoretic Quantum Algorithm for Solving Magic Squares

Variational quantum algorithms (VQAs) offer a promising near-term approach to finding optimal quantum strategies for playing non-local games. These games test quantum correlations beyond classical limits and enable entanglement verification. In this work, we present a variational framework for the Magic Square Game (MSG), a two-player non-local game with perfect quantum advantage. We construct a value Hamiltonian that encodes the game’s parity and consistency constraints, then optimize parameterize quantum circuits to minimize this cost. Our approach build on the stabilizer formalism, leverages commutation structure for circuit design, and is hardware-efficient. Compared to existing work, our contribution emphasizes algebraic structure an interpretability. We validate our method through numerical experiments and outline generalizations to larger games.

Chehade, Sarah [ORNL]↗
DOE OSTI2021

Structural, Electrical, and Electromechanical Properties of Inverse Hybrid Perovskites from First-Principles: The Case of (CH 3 NH 3 ) 3 OI

Inverse-hybrid perovskites (IHPs) with large polarization have recently been predicted from first-principles computations. Here, we use one representative from the IHP class of materials, (CH 3 NH 3 ) 3 OI (MA3OI), to propose a route to the first-principles prediction of structural and electrical properties, such as polarization, polarization reversibility, and the associated coercive field for hybrid organic–inorganic perovskites. The route relies on the construction of the polarization reversal path that models experimental measurements. Such a path was found to play an important role in the ground-state search as well as in the identification of competing structural variations. The latter is believed to be the origin of the structural disorder that is characteristic of hybrid organic–inorganic perovskites. The application of such an approach to MA3OI leads to the prediction of several structural variations that are expected to result in a structurally disordered phase above 766 K and of the polar ground state with a polarization of 25.3 μC/cm 2 that is reversible with the application of an electric field. The upper estimate for the coercive field associated with homogeneous polarization reversal is 6.9 GV/m. The piezoelectric constants of MA3OI are predicted to be an order of magnitude smaller in comparison with a prototypical inorganic ferroelectric PbTiO 3 ; however, the low symmetry of the MA3OI structure yields finite values for all components of the piezoelectric tensor. The polarization in MA3OI is tunable by the epitaxial strain (11.5% change under 5% epitaxial strain), although less so as compared with PbTiO 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Scalable Gradient Free Method for Bayesian Experimental Design with Implicit Models

Bayesian experimental design (BED) is to answer the question that how to choose designs that maximize the information gathering. For implicit models, where the likelihood is intractable but sampling is possible, conventional BED methods have difficulties in efficiently estimating the posterior distribution and maximizing the mutual information (MI) between data and parameters. Recent work proposed the use of gradient ascent to maximize a lower bound on MI to deal with these issues. However, the approach requires a sampling path to compute the pathwise gradient of the MI lower bound with respect to the design variables, and such a pathwise gradient is usually inaccessible for implicit models. In this paper, we propose a novel approach that leverages recent advances in stochastic approximate gradient ascent incorporated with a smoothed variational MI estimator for efficient and robust BED. Without the necessity of pathwise gradients, our approach allows the design process to be achieved through a unified procedure with an approximate gradient for implicit models. Several experiments show that our approach outperforms baseline methods, and significantly improves the scalability of BED in high-dimensional problems.

Zhang, Jiaxin↗
DOE OSTI2021

Graph Convolutional Network-Based Topology Embedded Deep Reinforcement Learning for Voltage Stability Control

Topological variations in power system is a common phenomenon and can impose significant challenges to traditional controllers of power system. Recent study revealed the strength of deep reinforcement learning (DRL) based approaches in power system preventive and corrective control. But topological variations are difficult to capture using classical fully connected neural network (FCN) model and has not been explicitly modeled in previous work. Hence, we develop a Graph Convolutional Network (GCN) based DRL framework to tackle topology changes in control design of power system. The GCN model exploits the graph structure of the power network and helps the DRL agent to embed the topology information during learning process. Our GCN based approach is evaluated using the IEEE-39 bus system and it outperforms the FCN-based DRL scheme in terms of training convergence and control performance considering grid topology changes.

Hossain, Ramij Raja↗
DOE OSTI2026

3D probabilistic fracture mechanics / computational fluid dynamics simulation of a reactor pressure vessel under transient conditions

Reactor pressure vessels (RPVs) are safety-critical light-water-reactor components that, under irradiation, experience long-term material degradation in the form of embrittlement. This can increase their susceptibility to fracture under thermal-shock conditions, which could occur during off-normal transients such as loss-of-coolant accidents (LOCAs). During a LOCA, the most severe conditions for the RPV occur when emergency core cooling water is injected through the cold legs into the water-and-steam-filled RPV. The rapid cooling of the downcomer and internal RPV surface causes decreased temperature and elevated thermally driven tensile stresses in the RPV wall. This, combined with long-term material embrittlement, may cause fracture initiation at pre-existing flaws, challenging the integrity of the RPV. Assessing RPV integrity during transients with a large spatial variation in the coolant temperature requires a modeling approach that considers the effects of spatially varying coolant temperature on the fracture probability of a population of flaws distributed throughout the RPV, accounting for spatially varying embrittlement. Here, the present study addresses this need by demonstrating first-of-its-kind coupling of a high-fidelity 3D computational fluid dynamics code with 3D probabilistic fracture mechanics This was accomplished using representative models of a pressurized-water reactor subjected to small- and medium-break LOCA conditions, both of which can result in large spatial temperature variations. While the observed impact of accounting for 3D effects was minimal under the small-break LOCA this study indicates a significant increase in the probability of fracture initiation under the medium-break LOCA when 3D effects are considered, relative to a spatially uniform cooling scenario.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Megadrought: A Series of Unfortunate La Niña Events?

Megadroughts are multidecadal periods of aridity more persistent than most droughts during the instrumental period. Paleoclimate evidence suggests that megadroughts occur in many parts of the world, including North America, Central America, western Europe, eastern Asia, and northern Africa. It remains unclear to what extent such megadroughts require external forcing or whether they can arise from internal climate variability alone. A novel statistical–dynamical approach is used to evaluate the possibility that such events arise solely as a function of interannual tropical sea surface temperature (SST) variations. A statistical emulator of tropical SST variations is constructed by using an empirical moving-blocks bootstrap approach that randomly samples multiyear sequences of the observational SST record. This approach preserves the power spectrum, seasonal cycle, and spatial pattern of El Niño-Southern Oscillation (ENSO) but removes longer timescale fluctuations embedded in the observational record. These resampled SST anomalies are then used to force an atmospheric model (the Community Atmosphere Model Version 5). As megadroughts emerge in this run, they should, therefore, be solely a consequence of La Niña sequences combined with internal atmospheric variability and persistence driven by soil moisture storage and other land-surface processes. We indeed find that megadroughts in this simulation have an amplitude-duration rate that is generally indistinguishable from the rate documented in paleoclimate records of the western United States. Our findings support the idea that megadroughts may occur randomly when the unforced climate system evolves freely over a sufficiently long period of time, implying that an unforced unusual but statistically plausible series of La Niña events may be sufficient to generate megadrought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Thermal dissipation sensors enter a new age: Navigating frontiers in transpiration and hydrologic function

Thermal dissipation (TD) sensors have been used extensively for a wide array of sap flow applications, and yet recently several limitations of this approach have been identified, including a tendency to underestimate absolute flows, especially in small stems with very high flows. However, when used properly, the TD method remains the most cost effective and reliable approach for determining relative flows in comparison studies. Major advantages of this method include the ability to replicate maximally within trees, across trees of different sizes, and across multiple species to capture the full range of natural variation in the study system. From early studies, such variation has been deemed a major challenge for representing stand-level dynamics. In a series of recent comparison studies, we determined mean sap flux density dynamics within and among groups of trees. These studies were conducted within temperate coniferous forest (n=46), temperate oak savanna (n=36), temperate pine forest (n=49), temperate bottomland hardwood forest (n=23), tropical premontane rainforest (n=43), semiarid subtropical shrubland (n=25), and tropical dry forest (n=15), with a total of 237 sensors. Two study sites were also equipped with eddy covariance systems for determination of stand-level evapotranspiration. Sites subject to high background thermal gradients used the transient thermal dissipation method. Comparisons varied between studies but tended to focus on relative flow differences between species, between wetter and drier microsites, between understory and overstory components, or between wetter and drier periods of the growing season. Except for the shrubland sites, study trees tended to be at least 15-cm diameter and frequently exceeded 50-cm diameter. Results of this cross-site comparison highlight the inherent variation in natural stands and the importance of using large sample sizes. The TD approach remains a valuable and preferred method for the future determination of water use in trees. However, sensor replication can fundamentally impact a study's outcomes and should be more carefully considered in study design. Customized error mitigation strategies are best to address the sources of variation most problematic for a particular study. In conclusion, the development of “smart” calibration approaches that correct for fundamental effects of radial variation inherent in thermal dissipation studies is discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Learning genetic perturbation effects with variational causal inference

Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional genomics and potentially for identifying therapeutic targets. Various computational models have been developed to predict perturbational effects. While deep learning models excel at interpolating observed perturbational data, they tend to overfit in the lack of enough data and may not generalize well to unseen perturbations. In contrast, mechanistic models, such as linear causal models based on gene regulatory networks, hold greater potential for extrapolation, as they encapsulate regulatory information that can predict responses to unseen perturbations. However, their application has been limited to small studies due to overly simplistic assumptions, making them less effective in handling noisy, large-scale single-cell data. We propose a hybrid approach that combines a mechanistic causal model with variational deep learning, termed Single Cell Causal Variational Autoencoder (SCCVAE). The mechanistic model employs a learned regulatory network to represent perturbational changes as shift interventions that propagate through the learned network. SCCVAE integrates this mechanistic causal model into a variational autoencoder, generating rich, comprehensive transcriptomic responses. Our results indicate that SCCVAE exhibits superior performance over current state-of-the-art baselines for extrapolating to predict unseen perturbational responses. Additionally, for the observed perturbations, the latent space learned by SCCVAE allows for the identification of functional perturbation modules and simulation of single-gene knockdown experiments of varying penetrance, presenting a robust tool for interpreting and interpolating perturbational responses at the single-cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigation of oscillations above the acoustic cut-off frequency for a sample of Kepler stars. II. Identifying temporal frequency shifts

ABSTRACT Stellar oscillations with frequencies greater than the acoustic cut-off frequency are not trapped within the star’s interior. Geometric interference between these high-frequency waves produces a peak-like structure in the power spectrum of the star, known as the pseudo-modes. In this study, we aim to analyse 51 stars previously identified (from a sample of 91 Kepler stars) to contain statistically significant evidence for pseudo-modes, to determine if the pseudo-mode frequencies vary in time. We obtained these frequency variations and the uncertainty by the resampled periodogram approach, where periodogram realisations were created from successive, overlapping 90-d time segments, and a cross-correlation function was generated between them. The computed shifts were compared against temporal p-mode frequency shifts and a stellar magnetic activity proxy, $S_{\mathrm{ph}}$. We found that for 16 per cent of the stars pseudo-mode frequency shifts were significantly anticorrelated with p-mode shifts, as is the case for the Sun. However, we also found pseudo-mode and p-mode shifts to be significantly correlated in-phase in 8 per cent of our sample. The remainder showed no significant correlation. We also searched for trends between the maximum variation of pseudo-mode frequency shifts and stellar parameters. Whilst we found no correlation between the maximum variation and stellar photospheric and chromospheric proxies, we found frequency variations to have a greater amplitude for cooler and slower rotating stars, which is in opposition to p-mode frequency shift variation. Temporal changes to pseudo-mode frequencies may be attributable to variations in stellar magnetic activity, and therefore can contribute to our understanding of stellar activity cycles.

Millson, L. J. (ORCID:0009000342542676)↗
DOE OSTI2022

Inverse Analysis with Variational Autoencoders: A Comparison of Shallow and Deep Networks

Inverse problems are applied to determine unknown properties by matching observational data with a physical model that often takes many parameters as input. To overcome the underconstrained nature of inverse problems and achieve good performance, an approach is presented involving regularization with a technique known as a variational autoencoder (VAE), which is trained to map a high-dimensional parameter space with a complex structure to a low-dimensional latent space with a simple structure. We apply this approach to unconditioned realizations of the parameters (heterogeneous hydraulic fields) for a hydrogeological inverse problem. Two types of hydraulic conductivity fields are used to evaluate the characterization for the different levels of heterogeneity complexity of the physical inputs. This approach keeps the computational cost of generating the training data low. The reason is unconditioned realizations neither rely on the observational data used to perform the inverse analysis nor require any groundwater flow model forward runs. In addition, this approach applies regularization on a low-dimensional latent space from the VAE and increases optimization efficiency through automatic differentiation. Furthermore, two different neural network (NN) structures are tested for their utility in using the VAE for inverse analysis. The performance of a deep, convolutional neural network strongly depends on the dimensionality of the latent space, which requires tuning. In contrast, a shallow, dense neural network provides consistently accurate characterization without tuning. Furthermore, our approach evaluates the advantages of the shallow, dense neural network over the deep, convolutional one and enables future application to a wide range of inverse problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The Role of State Utility Regulators in a Just and Reasonable Energy Transition: Examining Regulatory Approaches to the Economic Impacts of Coal Retirements

The ongoing trend of coal retirements has disproportionately affected the socioeconomic health of communities where power plants are located. For many public utility commissions, these impacts have led to important questions around the scope of PUCs’ statutory authority to analyze, consider and mitigate losses to host communities within their role as utility regulators. Due largely to variations in state legislative charges, commissions have taken different approaches to articulating what lies within the public interest.This report examines the authority of PUCs across the country to consider non-energy economic impacts beyond direct ratepayer effects, and summarizes approaches that PUCs, utilities and other stakeholders have used to mitigate the economic fallout of coal retirements, specifically.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

The entropy of galaxy spectra: how much information is encoded?

Abstract The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.

Ferreras, Ignacio (ORCID:0000000345843127)↗
DOE OSTI2024

An explainable variational autoencoder model for three-dimensional acoustic emission source localization in hollow cylindrical structures

We introduce an explainable variational autoencoder for three-dimensional (3D) localization of acoustic emission sources in hollow cylindrical structures, with an unsupervised approach. This research capitalizes on multi-arrival waveforms generated by helical path propagation in cylindrical geometries to enable efficient two-receiver localization. By integrating the modal characteristics of Lamb modes under multi-path conditions, we demonstrate that two sets of time-of-arrival differences and peak amplitudes extracted from one receiver can serve as effective localization features. This initial approach identifies four potential source locations, highlighting the feasibility of two-receiver source localization using traditional feature extraction methods. However, direct extraction can be challenging when mode overlaps occur, complicating the localization process. To address this, our work proposes a novel waveform-based method. This method leverages the consistent dispersion characteristics within isotropic materials, where each unique combination of mode arrival times and peak amplitudes constructs a distinct waveform. This distinctiveness overcomes the ambiguities associated with mode overlaps, significantly enhancing the method’s precision and robustness. Our approach adopts a data-driven strategy for waveform-based localization using variational autoencoder (VAE). VAE discerns waveform patterns for localization, while also addressing data uncertainties. The VAE’s encoder and decoder networks capture the localization process and the source’s influence on waveform generation, respectively, guiding latent variables to segregate waveforms by source in the latent space. The design of the learning process focuses on specific localization characteristics to enhance result explainability. Localization predictions are generated by projecting test waveforms, not included in the training set, onto a trained latent space. The prediction is determined using a nearest-neighbor approach based on the closest latent representation of a source. Validation with pencil-lead-break tests on a metallic pipe confirmed our method’s effectiveness, achieving an averaged 3D localization accuracy of 0.84.

Lee, Guan-Wei↗
DOE OSTI2020

A generalized approximate control variate framework for multifidelity uncertainty quantification

We describe and analyze a variance reduction approach for Monte Carlo (MC) sampling that accelerates the estimation of statistics of computationally expensive simulation models using an ensemble of models with lower cost. These lower cost models — which are typically lower fidelity with unknown statistics — are used to reduce the variance in statistical estimators relative to a MC estimator with equivalent cost. We derive the conditions under which our proposed approximate control variate framework recovers existing multifidelity variance reduction schemes as special cases. We demonstrate that existing recursive/nested strategies are suboptimal because they use the additional low-fidelity models only to efficiently estimate the unknown mean of the first low-fidelity model. As a result, they cannot achieve variance reduction beyond that of a control variate estimator that uses a single low-fidelity model with known mean. However, there often exists about an order-of-magnitude gap between the maximum achievable variance reduction using all low-fidelity models and that achieved by a single low-fidelity model with known mean. We show that our proposed approach can exploit this gap to achieve greater variance reduction by using non-recursive sampling schemes. The proposed strategy reduces the total cost of accurately estimating statistics, especially in cases where only low-fidelity simulation models are accessible for additional evaluations. Several analytic examples and an example with a hyperbolic PDE describing elastic wave propagation in heterogeneous media are used to illustrate the main features of the methodology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗