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DOE OSTI2025

Machine learning for fundamental spectroscopic and thermodynamic data of actinides and lanthanides

Accurately modeling optical spectra with absolute radiometric intensities is vital for nuclear forensics applications that depend on characterizing optical emissions from energetic nuclear phenomena. This requires precise knowledge of the individual atomic transition probabilities, known as Einstein A-coefficients, for each emission line. Obtaining these values theoretically or experimentally is often impractical due to the complex electronic structures and the number of transitions involved in atoms relevant to nuclear applications. In this study, we explore the use of machine learning to predict the Einstein A coefficients for atomic transitions. Seven models were evaluated that ranged from deep learning to decision tree algorithms, and found that gradient boosting performed best, specifically the Extreme Gradient Boosting (XGB) architecture, achieving a precision of 86% across transitions of 36 elements. Furthermore, the model was cross-validated using published transition probabilities reported in the literature and applied to estimate Pu plasma temperatures from a previous experiment conducted at Savannah River National Laboratory.

Atomic spectroscopy↗

DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Beyond Price Taker: Conceptual Design and Optimization of Integrated Energy Systems Using Machine Learning Market Surrogates

Future electricity generation systems must be optimized to provide flexibility that counteracts the variability of non-dispatchable renewable energy sources and ensures the reliability and safety of critical infrastructure, including the electric grid. The current state-of-the-art is to co-optimize the design and operation of integrated energy systems (IES) treating historical or predicted time-series electricity prices as fixed parameters. Recent literature has shown the limitations of this price taker assumption, which neglects how IES optimization decisions influence market outcomes. As such, this paper proposes a new optimization formulation that uses machine learning surrogate models, trained from a library of annual market operation simulations, to embed IES market interactions into the co-optimization problem directly. Using a thermal generator example built in the open-source IDAES computational environment, we show that the price taker approach routinely over-predicts annual revenues by 8% or more compared to a validation simulation, where the proposed approach has a typical relative error of 1% or less.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Technical Advances for Sustainable Remediation: In Situ Monitoring and Climate Resiliency - 18436

Recent advances in sustainable remediation techniques show promise as solutions for contaminant removal in soil and groundwater media. Although passive remediation (or natural attenuation) has gained momentum as an acceptable technique, there are still challenges in regulatory frameworks as well as in public acceptance. Leaving contaminants in subsurface requires increased burden of proof to show that plumes are stable and residual contaminants do not pose a significant health risk. Climate changes and frequent extreme climate events contribute another level of complexity and make it difficult to demonstrate system stability and predict future plume conditions. In this study, we show two coupled approaches to tackle this challenge: (1) in situ groundwater monitoring based on advanced sensor and data analytics technologies (i.e., Big Data), and (2) state-of-art modeling for optimizing monitoring and site closure strategies. In the new monitoring approach, in situ sensors are used to continuously measure the key variables that control contaminant plume mobility and its spatial and temporal distribution (such as pH, redox potential, electrical conductivity, and groundwater level). Coupled with a limited number of groundwater sampling, the data analytics methods - data mining and machine learning - allow us to estimate contaminant concentrations, and also to detect any significant changes associated with the plume mobility. In parallel, the state-of-art numerical flow and reactive transport model - ASCEM software under DOE Office of Environmental Management - provides a physical and mechanistic understanding of the system behavior, and predicts the long-term plume migration for optimizing the monitoring and closure strategies. In particular, we focus on the effects of extreme precipitation or drought on the site closure as well as monitoring strategies. We demonstrate this approach at the Savannah River Site (SRS) F-Area, where groundwater is contaminated by various radionuclides, including uranium, tritium and technetium. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Defect Complexes in CrSBr Revealed Through Electron Microscopy and Deep Learning

Atomic defects underpin the properties of van der Waals materials, and their understanding is essential for advancing quantum and energy technologies. Scanning transmission electron microscopy is a powerful tool for defect identification in atomically thin materials, and extending it to multilayer and beam-sensitive materials would accelerate their exploration. Here, we establish a comprehensive defect library in a bilayer of the magnetic quasi-1D semiconductor CrSBr by combining atomic-resolution imaging, deep learning, and calculations. We apply a custom-developed machine learning work flow to detect, classify, and average point vacancy defects. This classification enables us to uncover several distinct Cr interstitial defect complexes, combined Cr and Br vacancy defect complexes, and lines of vacancy defects that extend over many unit cells. We show that their occurrence is in agreement with our computed structures and binding energy densities, reflecting the intriguing layer interlocked crystal structure of CrSBr. Our ab initio calculations show that the interstitial defect complexes give rise to highly localized electronic states. These states are of particular interest due to the reduced electronic dimensionality and magnetic properties of CrSBr and are, furthermore, predicted to be optically active. Our results broaden the scope of defect studies in challenging materials and reveal new defect types in bilayer CrSBr that can be extrapolated to the bulk and to over 20 materials belonging to the same FeOCl structural family.

deep learning↗

DOE OSTI2025

Single-qubit multi-party transmission using universal symmetric quantum cloning

This study considers the hypothetical quantum network case where Alice wishes to transmit one qubit of information (specifically a pure quantum state) to M parties, where M is some large number. The remote receivers locally perform single-qubit quantum state tomography on the transmitted qubits in order to compute the quantum state within some error rate (dependent on the tomography technique and the number of transmitted qubits). We show that with the use of an intermediate optimal symmetric universal quantum cloning machine (between Alice and the remote receivers) as a repeater-type node in a hypothetical quantum network, Alice can send significantly fewer qubits compared to direct transmission of the message qubits to each of the M remote receivers. This is possible due to two properties of quantum cloning. The first is that single qubit quantum clones retain the same Bloch angle as the initial quantum state. This means that if the mixed state of the quantum clone can be computed to high enough accuracy, the original pure quantum state can be inferred by extrapolating that vector to the surface of the Bloch sphere. The second property is that the state overlap of approximate quantum clones, with respect to the original pure quantum state, quickly converges (specifically for 1 → M , the limit of the fidelity as M goes to infinity is $\frac{2}{3}$). This means that Alice can prepare a constant number of qubits (which are then passed through the quantum cloning machine) in order to achieve a desired error rate if M is large enough. Combined, these two properties mean that for a large M , Alice can prepare many orders of magnitude fewer qubits in order to achieve the same single qubit transmission accuracy compared to the naive direct qubit transmission approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

International Workshop on Electronic Structure 2024 (ES 24)

The 36th annual Workshop on Recent Developments in Electronic Structure Theory commenced on June 2-5, 2024 at Boston University with 136 in-person and 75 virtual attendees. The organizing committee was composed of five faculty at Boston University with seven local area faculty comprising the greater Boston area advisory committee. On the first day, two hands-on workshops, NEXMD and ComDMFT were held on June 2, two full days of presentations were held on June 3-4 and one half day on June 5. There were 19 invited speakers who spoke about the state-of-the-art in electronic structure methods, including density functional theory, many-body perturbation theory, and the incorporation of machine learning into electronic structure calculations. In addition, 45 young scientists presented posters on June 4. Housing at a reduced rate was provided at the Boston University dormitories. This conference provided a valuable opportunity for scientists, students, postdocs, and senior researchers alike, to disseminate their latest research results, discuss their ideas and best practices, learn from each other, and form new collaborations.

42 ENGINEERING↗

DOE OSTI2025

Machine-learning-informed scattering correlation analysis of sheared colloids

We have carried out theoretical analysis, Monte Carlo simulations and machine-learning analysis to quantify microscopic rearrangements of dilute dispersions of spherical colloidal particles from coherent scattering intensity. Both monodisperse and polydisperse dispersions of colloids were created and underwent a rearrangement consisting of an affine simple shear and non-affine rearrangement using the Monte Carlo method. We calculated the coherent scattering intensity of the dispersions and the correlation function of intensity before and after the rearrangement and generated a large data set of angular correlation functions for varying system parameters, including number density, polydispersity, shear strain and non-affine rearrangement. Singular value decomposition of the data set shows the feasibility of machine-learning inversion from the correlation function for the polydispersity, shear strain and non-affine rearrangement using only three parameters. A Gaussian process regressor is then trained on the data set and can retrieve the affine shear strain, non-affine rearrangement and polydispersity with relative errors of 3%, 1% and 6%, respectively. Altogether, our model provides a framework for quantitative studies of both steady and non-steady microscopic dynamics of colloidal dispersions using coherent scattering methods.

Gaussian process regression↗

DOE OSTI2021

Non-intrusive nonlinear model reduction via machine learning approximations to low-dimensional operators

Abstract Although projection-based reduced-order models (ROMs) for parameterized nonlinear dynamical systems have demonstrated exciting results across a range of applications, their broad adoption has been limited by their intrusivity: implementing such a reduced-order model typically requires significant modifications to the underlying simulation code. To address this, we propose a method that enables traditionally intrusive reduced-order models to be accurately approximated in a non-intrusive manner. Specifically, the approach approximates the low-dimensional operators associated with projection-based reduced-order models (ROMs) using modern machine-learning regression techniques. The only requirement of the simulation code is the ability to export the velocity given the state and parameters; this functionality is used to train the approximated low-dimensional operators. In addition to enabling nonintrusivity, we demonstrate that the approach also leads to very low computational complexity, achieving up to $$10^3{\times }$$ 10 3 × in run time. We demonstrate the effectiveness of the proposed technique on two types of PDEs. The domain of applications include both parabolic and hyperbolic PDEs, regardless of the dimension of full-order models (FOMs).

42 ENGINEERING↗

DOE OSTI2026

The macroevolution of filamentation morphology across the Saccharomycotina yeast subphylum

Saccharomycotina is a subphylum of ascomycete fungi with diverse asexual growth morphologies. Filamentous growth can comprise linear and branched budding cells that do not undergo cell separation, termed pseudohyphae, or tubular filaments with septa that perforate allowing movement of organelles, termed true hyphae. We integrated phenotypic, genomic, metabolic, and environmental data on isolation sources from 1051 species to examine the variation and evolutionary history of filamentation across Saccharomycotina and determine whether these data could predict filamentation types. We found that 63.37% of strains can form filaments; 6.56% true hyphae, 42.40% pseudohyphae, and 14.39% both true hyphae and pseudohyphae. The distributions of species that can produce true hyphae or filament were more strongly correlated with the yeast phylogeny than the distribution of species with pseudohyphae. Ancestral state reconstruction suggested that true hyphal and pseudohyphal morphologies evolved several times, that most yeast ancestors likely produced pseudohyphae or lacked filaments, and that the Saccharomycotina last common ancestor likely produced pseudohyphae but not true hyphae. Machine learning models trained on genomic and metabolic features predicted filament morphologies with ∼70% accuracy. Connecting the evolution of morphologies to their genomic, physiological, and ecological characteristics will enrich our understanding of how the diversity of lifestyles evolved in Saccharomycotina.

Saccharomycotina↗

DOE OSTI2018

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks. The rapid growth of single-cell sequencing data has greatly stimulated applications of statistical and machine learning methods for inferring topologies of pluripotency regulating genetic networks. The inferred network topologies, however, often only encode Boolean information while remaining silent about the roles of dynamics and molecular stochasticity inherent in gene expression. Herein we develop a framework for systematically extending Boolean-level network topologies into higher resolution models of networks which explicitly account for the promoter architectures and gene state switching dynamics. We show the framework to be useful for disentangling the various contributions that gene switching, external signaling, and network topology make to the global heterogeneity and dynamics of transcription factor populations. We find the pluripotent state of the network to be a steady state which is robust to global variations of gene switching rates which we argue are a good proxy for epigenetic states of individual promoters. The temporal dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the rates of genetic switching which makes cells more responsive to changes in extracellular signals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

AWE-ML: Averaged Weights for Explainable Machine Learning v. 1.0

This software uses averaged weighted estimators to classify instances and then explicate the individual decision process in classification. The software has state of the art performance in accuracy, while maintaining full explainability. It does this by calculating hierarchically averaged probabilities for a large class of feature combinations and updating them ‘on-the-fly’. On the fly updating also allows the model to be accurate, relative to the total dataset, maintaining accuracy in real-time, without a need to retrain the classifier.

Agarwal, Sapan↗

DOE OSTI2023

Machine-learning-based spectral methods for partial differential equations

Spectral methods are an important part of scientific computing’s arsenal for solving partial differential equations (PDEs). However, their applicability and effectiveness depend crucially on the choice of basis functions used to expand the solution of a PDE. The last decade has seen the emergence of deep learning as a strong contender in providing efficient representations of complex functions. In the current work, we present an approach for combining deep neural networks with spectral methods to solve PDEs. In particular, we use a deep learning technique known as the Deep Operator Network (DeepONet) to identify candidate functions on which to expand the solution of PDEs. We have devised an approach that uses the candidate functions provided by the DeepONet as a starting point to construct a set of functions that have the following properties: (1) they constitute a basis, (2) they are orthonormal, and (3) they are hierarchical, i.e., akin to Fourier series or orthogonal polynomials. We have exploited the favorable properties of our custom-made basis functions to both study their approximation capability and use them to expand the solution of linear and nonlinear time-dependent PDEs. The proposed approach advances the state of the art and versatility of spectral methods and, more generally, promotes the synergy between traditional scientific computing and machine learning.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Role of Wadsley Defects and Cation Disorder to Enhance MoNb 12 O 33 Diffusion

Wadsley-Roth (WR) niobates have emerged as high-rate anode materials that can combine rapid ionic diffusion with good electronic conductivity. WR compounds have been defect-enhanced by limited annealing, however, such materials often contain multiple types of defects. In particular, both Wadsley defects (variable block size) and transition metal disorder have the potential to modify transport rates, however the corresponding effects are not well understood mechanistically. Here, MoNb 12 O 33 (MNO) was calcined at two different temperatures to compare a defect-rich condition (MNO-800) with a proximal order-rich condition (MNO-900) as assessed through XRD, XANES, EXAFS, and STEM characterizations. Galvanostatically cycled lithium half cells of MNO-800 exhibited additional capacity (307 mAhg −1 at 0.1C, 4.66% higher) and improved high-rate capacity of 200 mAhg −1 at 10C. ICI-based overpotential analysis identified solid state diffusion as the dominant rate limiting process where MNO-800 correspondingly exhibited ∼3X faster capacity-weighted diffusivity. A machine-learning interatomic potential was trained to density functional theory and then applied with molecular dynamics (MLIP-MD) to examine the possible roles of Wadsley defects and transition metal disorder. For both defect-types, Li was found to populate and activate fast diffusion paths from window sites at lower extents of lithiation as compared to the order-rich model.

defect↗

DOE OSTI2024

Applying machine learning and quantum chemistry to predict the glass transition temperatures of polymers

Glass transition temperature (T g ) is important for understanding the physical and mechanical properties of a polymer material because it relates to the thermal energy required to transition between a hard glassy state and a soft rubbery one. Over the years, various models have been developed for predicting this thermal property from molecular structure to aid in designing novel polymers in selected classes. This work builds on those efforts by utilizing both machine learning (ML) and quantum chemistry (QC) techniques to develop models that can predict T g values from the molecular structure under different data availability scenarios and for a wide variety of polymer types. For the ML model, a graph convolutional network (GCN) was used to map topological polymer features; this model was trained against a dataset of more than 7500 T g values and resulted in a root mean square error (RMSE) of 38.1 °C. The QC-based regression model was trained on 83 T g values and produced an RMSE of 34.5 °C. In conclusion, this work demonstrated that while both model techniques produce accurate predictions and are suitable for different data availability scenarios, the QC-based regression model offered a more interpretable model framework with significantly less training data.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Exploring the formation of gold/silver nanoalloys with gas-phase synthesis and machine-learning assisted simulations

While nanoalloys are of paramount scientific and practical interest, the main processes leading to their formation are still poorly understood. Key structural features in the alloy systems, including the crystal phase, chemical ordering, and morphology, are challenging to control at the nanoscale, making it difficult to extend their use to industrial applications. Here, in this contribution, we focus on the gold/silver system that has two of the most prevalent noble metals and combine experiments with simulations to uncover the formation mechanisms at the atomic level. Nanoparticles were produced using a state-of-the-art inert-gas aggregation source and analyzed using transmission electron microscopy and energy-dispersive X-ray spectroscopy. Machine-learning-assisted molecular dynamics simulations were employed to model the crystallization process from liquid droplets to nanocrystals. Our study finds a preponderance of nanoparticles with five-fold symmetric morphology, including icosahedra and decahedra which is consistent with previous results on mono-metallic nanoparticles. However, we observed that gold atoms, rather than silver atoms, segregate at the surface of the obtained nanoparticles for all the considered alloy compositions. These segregation tendencies are in contrast to previous studies and have consequences on the crystallization dynamics and the subsequent crystal ordering. We finally showed that the underpinning of this surprising segregation dynamics is due to charge transfer and electrostatic interactions rather than surface energy considerations.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Bottom-up design of actinide materials from molecular clusters: Demonstration of a general-purpose simulation capability leveraging machine-learned atomic potentials

Actinide thin-film coatings such as uranium dioxide (UO 2 ) play an important role in nuclear reactors and other mission-relevant applications, but realization of their potential requires a deep fundamental understanding of the chemical vapor deposition (CVD) processes used for their growth. The slow experimental progress can be attributed, in part, to the standard safety guidelines associated with handling uranium byproducts, which are often corrosive, toxic, and radioactive. Accurate simulation techniques, when used in concert with experiment, can improve laboratory safety, material durability, and deliverable timeframes. However, state-of-the-art computational methods are either insufficiently accurate or intractably expensive. To remedy this situation, in this project we suggested a machine-learning (ML) accelerated workflow for simulating molecular clustering toward deposition. As a benchmark test case, we considered molecular clustering in steam and assessed independent components of our workflow by comparing with measured thermodynamic properties of water. After analyzing each component individually and finding no fundamental barrier to realization of the workflow, we attempted to integrate the ML component, a Sandia-developed tool called FitSNAP. As this was the first application of FitSNAP to atoms and molecules in the gas phase at Sandia, the method required more fitting data than was originally anticipated. Systematic improvements were made by including in the fit data diatomic potentials, molecular single-bond-breaking curves, and symmetry-constrained intermolecular potentials. We concluded that our strategy provides a feasible pathway toward modeling CVD and related processes, but that extensive training data must be generated before it can be of practical use.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor

High-resolution crystal structures together with mutational analysis and transient kinetics experiments were utilized to understand nucleotide sensing and the regulation of the ATPase cycle in an AAA+ molecular motor. ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg{sup 2+} ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗