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DOE OSTI2025

Active deep kernel learning of molecular properties from structural embeddings

As vast databases of chemical identities become increasingly available, the challenge shifts to how we effectively explore and leverage these resources to study molecular properties. This paper presents an active learning approach for molecular discovery using deep kernel learning (DKL), demonstrated on the QM9 dataset. DKL links structural embeddings directly to properties, creating organized latent spaces that prioritize relevant property information. By iteratively recalculating embedding vectors in alignment with target properties, DKL uncovers concentrated maxima representing key molecular properties and reveals unexplored regions with potential for innovation. This approach underscores DKL’s potential in advancing molecular research and discovery.

Artificial neural networks↗

DOE OSTI2020

Creation of a High-Yield AAV Vector Production Platform in Suspension Cells Using a Design-of-Experiment Approach

Recombinant adeno-associated virus (rAAV) vectors are a leading gene delivery platform, but vector manufacturing remains a challenge. New methods are needed to increase rAAV yields and reduce costs. Past efforts to improve rAAV production have focused on optimizing a single variable at a time, but this approach does not account for the interactions of multiple factors that contribute to vector generation. Here, we utilized a design-of-experiment (DOE) methodology to optimize rAAV production in a HEK293T suspension cell system. We simultaneously varied the transgene, packaging, and helper plasmid ratios, the total DNA concentration, and the cell density to systematically evaluate the impact of each variable across 52 conditions. The results revealed a unique set of parameters with a lower concentration of transgene plasmid, a higher concentration of packaging plasmid, and a higher cell density than previously described protocols. Using this DOE-optimized protocol, we achieved unpurified yields approaching 3 × 10 14 viral genomes (VGs)/L of cell culture. Additionally, we incorporated polyethylene glycol (PEG)-based virus precipitation, pH-mediated protein removal, and affinity chromatography to our downstream processing, enabling average purified yields of >1 × 10 14 VGs/L for rAAV-EGFPs across 13 serotypes and capsid variants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Prediction of Gibbsite Precipitation for LAWPS and TSCR Processes at Hanford (U)

Determining the risk of precipitation of feed streams that could potentially lead to plugging ion exchange columns resulting in potential safety concerns and inefficient operation. Characterizing the feed to the filter at the Hanford site and compare it to the feed stream at SRS in ARP-MCU. Different precipitation distribution was observed for Hanford and SRS sites. Gibbsite precipitation is strongly affected by hydroxide concentration and temperature. High degrees of uncertainty of prediction of the exact amount of precipitate due to the extreme sensitivity of the waste solution to hydroxide fluctuations. Overall TSCR system consists of transferring supernate into an existing tank farm tank. Upon sampling and feed qualification, the supernate is sent into a dead-end filter to remove entrained solids, then is passed through an ion exchange column. The treated supernate will then be sent into another tank farm tank which will be used as the feed to the LAW vitrification facility. 250 + projected feed batches provided by Hanford: Reduced down to 65 batches; Projecting the feed vector from 2021-2054. Differences in Hanford and Savannah River waste feed stream compositions leading to dissimilar ionic interactions thus different precipitation distributions. Gibbsite: Dominating precipitate in Hanford waste (89 %). Sodium Oxalate: Predominant precipitate in SRS Waste (84 %). Based on the results, gibbsite precipitation is inversely affected by hydroxide concentration and temperature. Risk of precipitation is highly sensitive to hydroxide concentration and can vary significantly with slight fluctuations. All 65 batches showed distinct results with the range of [0.14, 1.25] Vol % and [0.28, 1.92] Mass % PPT.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

A machine learning approach to water quality forecasts and sensor network expansion: Case study in the Wabash River Basin, United States

Abstract Midwestern cities require forecasts of surface nitrate loads to bring additional treatment processes online or activate alternative water supplies. Concurrently, networks of nitrate monitoring stations are being deployed in river basins, co‐locating water quality observations with established stream gauges. However, tools to evaluate the future value of expanded networks to improve water quality forecasts remains challenging. Here, we construct a synthetic data set of stream discharge and nitrate for the Wabash River Basin—one of the United States’ most nutrient polluted basins—using the established Agro‐IBIS and THMB models. Synthetic data enables rapid, unbiased and low‐cost assessment of potential sensor placements to support management objectives, such as near‐term forecasting. Using the synthetic data, we established baseline 1‐day forecasts for surface water nitrate at 12 cities in the basin using support vector machine regression (SVMR; RMSE 0.48–3.3 ppm). Next, we used the SVMRs to evaluate the improvement in forecast performance associated with deployment of additional nitrate sensors. We identified the optimal sensor placement to improve forecasts at each city, and the relative value of sensors at each candidate location. Finally, we assessed the co‐benefit realized by other cities when a sensor is deployed to optimize a forecast at one city, finding significant positive externalities in all cases. Ultimately, our study explores the potential for machine learning to make near‐term predictions and critically evaluate the improvement realized by expanding a monitoring network. While we use nitrate pollution in the Wabash River Basin as a case study, this approach could be readily applied to any problem where the future value of sensors and network design are being evaluated.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Dispersion relations for γγ → ππ: helicity amplitudes, subtractions, and anomalous thresholds

We present a comprehensive analysis of the dispersion relations for the doubly-virtual process γ * γ * → ππ . Starting from the Bardeen-Tung-Tarrach amplitudes, we first derive the kernel functions that define the system of Roy-Steiner equations for the partial-wave helicity amplitudes. We then formulate the solution of these partial-wave dispersion relations in terms of Omnès functions, with special attention paid to the role of subtraction constants as critical for the application to hadronic light-by-light scattering. In particular, we explain for the first time why for some amplitudes the standard Muskhelishvili-Omnès solution applies, while for others a modified approach based on their left-hand cut is required unless subtractions are introduced. In the doubly-virtual case, the analytic structure of the vector-resonance partial waves then gives rise to anomalous thresholds, even for space-like virtualities. We develop a strategy to account for these effects in the numerical solution, illustrated in terms of the D -waves in γ * γ * → ππ , which allows us to predict the doubly-virtual responses of the f 2 (1270) resonance. In general, our results form the basis for the incorporation of two-meson intermediate states into hadronic light-by-light scattering beyond the S -wave contribution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Xylella fastidiosa modulates exopolysaccharide polymer length and the dynamics of biofilm development with a β-1,4-endoglucanase

Xylella fastidiosa is a Gram-negative bacterium that causes disease in many economically important crops. It colonizes the plant host xylem and the mouthparts of its insect vectors where it produces exopolysaccharide (EPS) and forms robust biofilms. Typically, the ability to form a biofilm enhances virulence, but X. fastidiosa does not fit neatly into that paradigm. Instead, X. fastidiosa enters into biofilms to attenuate its movement in the xylem, which, in turn, slows disease progression. In most of its over 600 known plant hosts, X. fastidiosa behaves as a benign commensal, but in some hosts like Vitis vinifera grapevines, it acts as a pathogen. Its ability to attenuate its own virulence in susceptible hosts may be a remnant of its commensal lifestyle in other hosts. Here, we demonstrate that X. fastidiosa utilizes a β-1,4 endoglucanase to cleave its self-produced β-1,4-glucan exopolysaccharide polymer to process it from a higher molecular weight to a lower molecular weight polymer. This processing mediates surface adherence of the cells and ultimately governs overall biofilm architecture, indicating enzymatic pruning of the EPS plays a key role in biofilm-mediated attenuation of X. fastidiosa in planta and, thus, is a key vestige that links its commensal behaviors to its parasitic behaviors in specific hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Practical CO2—WAG Field Operational Designs Using Hybrid Numerical-Machine-Learning Approaches

Machine-learning technologies have exhibited robust competences in solving many petroleum engineering problems. The accurate predictivity and fast computational speed enable a large volume of time-consuming engineering processes such as history-matching and field development optimization. The Southwest Regional Partnership on Carbon Sequestration (SWP) project desires rigorous history-matching and multi-objective optimization processes, which fits the superiorities of the machine-learning approaches. Although the machine-learning proxy models are trained and validated before imposing to solve practical problems, the error margin would essentially introduce uncertainties to the results. In this paper, a hybrid numerical machine-learning workflow solving various optimization problems is presented. By coupling the expert machine-learning proxies with a global optimizer, the workflow successfully solves the history-matching and CO2 water alternative gas (WAG) design problem with low computational overheads. The history-matching work considers the heterogeneities of multiphase relative characteristics, and the CO2-WAG injection design takes multiple techno-economic objective functions into accounts. This work trained an expert response surface, a support vector machine, and a multi-layer neural network as proxy models to effectively learn the high-dimensional nonlinear data structure. The proposed workflow suggests revisiting the high-fidelity numerical simulator for validation purposes. The experience gained from this work would provide valuable guiding insights to similar CO2 enhanced oil recovery (EOR) projects.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Measurement of the cross section for electroweak production of a Z boson, a photon and two jets in proton-proton collisions at $\sqrt{s} =$ 13 TeV and constraints on anomalous quartic couplings

A measurement is presented of the cross section for electroweak production of a Z boson and a photon in association with two jets (Zγjj) in proton-proton collisions. The Z boson candidates are selected through their decay into a pair of electrons or muons. The process of interest, electroweak Zγjj production, is isolated by selecting events with a large dijet mass and a large pseudorapidity gap between the two jets. The measurement is based on data collected at the CMS experiment at $ \sqrt{s} $ = 13 TeV, corresponding to an integrated luminosity of 35.9 fb$^{−1}$. The observed significance of the signal is 3.9 standard deviations, where a significance of 5.2 standard deviations is expected in the standard model. These results are combined with published results by CMS at $ \sqrt{s} $ = 8 TeV, which leads to observed and expected respective significances of 4.7 and 5.5 standard deviations. From the 13 TeV data, a value is obtained for the signal strength of electroweak Zγjj production and bounds are given on quartic vector boson interactions in the framework of dimension-eight effective field theory operators.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Far-from-equilibrium slow modes and momentum anisotropy in expanding plasma

The momentum distribution of particle production in heavy-ion collisions encodes information about thermalization processes in the early-stage quark-gluon plasma. We use kinetic theory to study the far-from-equilibrium evolution of an expanding plasma with an anisotropic momentumspace distribution. We identify slow and fast degrees of freedom in the far-from-equilibrium plasma from the evolution of moments of this distribution. At late times, the slow modes correspond to hydrodynamic degrees of freedom and are naturally gapped from the fast modes by the inverse of the relaxation time, $τ$$^{–1}_{R}$. At early times, however, there are an infinite number of slow modes with a gap inversely proportional to time, τ –1 . From the evolution of the slow modes we generalize the paradigm of the far-from-equilibrium attractor to vector and tensor components of the energy momentum tensor, and even to higher moments of the distribution function that are not part of the hydrodynamic evolution. We predict that initial-state momentum anisotropy decays slowly in the far-from-equilibrium phase and may persist until the relaxation time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Leveraging machine learning to enhance aerosol classification using Single-Particle Mass Spectrometry

Advancing automated classification of atmospheric aerosols from Single-Particle Mass Spectrometry (SPMS) data remains challenging due to overlapping ion signatures, compositional diversity, and limited labeled data. This study evaluates supervised and semi-supervised learning frameworks to enhance aerosol identification by jointly leveraging labeled and unlabeled spectra. Four models were compared: a supervised Support Vector Machine (SVM), a self-training SVM, a stacked autoencoder classifier, and a stacked autoencoder trained using a temporal-ensembling Mean Teacher approach. All models achieved high and stable accuracies (90.0 %–91.1 %), surpassing previous results on the same dataset (87 %) and matching the performance of state-of-the-art deep learning methods. Despite small global metric differences (≤ 1 %), semi-supervised variants yielded up to 5 %–10 % improvements for compositionally rare particle types – such as soot (0.77 % of spectra, F1-score: 0.93–0.97) and hazelnut pollen (0.98 % of spectra, F1-score: 0.97–1.00) – equating to roughly ∼ 187 additional correctly classified spectra. These gains are scientifically significant, as such rare particles exert disproportionate influence on radiative absorption and ice nucleation processes; their improved detection reduces modeled uncertainties in aerosol absorption optical depth and mixed-phase cloud ice nucleation rates. The models' residual misclassifications (≈ 9 %) largely arise from true spectral overlap among chemically adjacent species (e.g., Na- vs. K-feldspar, coated vs. uncoated feldspars), reflecting physical compositional continuity rather than algorithmic error. Collectively, these findings demonstrate that leveraging unlabeled data to learn robust spectral representations and refine classification enhances both fidelity and interpretability, bridging data-driven analysis with aerosol–climate process understanding.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Predicting melt pool depth and grain length using multiple signatures from in-situ single camera two-wavelength imaging pyrometry for laser powder bed fusion

In laser powder bed fusion (LPBF), the in-situ process signatures are known to have a direct correlation with the microstructural properties of the solidified melt pool (MP). It is known that the MP cooling and heating rates, and laser processing parameters can critically determine the grain structure and thereby affect the part properties. The objective of this work is to study the feasibility of using in-process, high-speed imaging pyrometry for evaluating the solidified MP properties “below” the surface, such as depth and microstructural properties. To accomplish this, we employ an in-house single camera-based two-wavelength imaging pyrometry (STWIP) system for monitoring the printing of single-scan tracks with Inconel 718 on a commercial LPBF printer (EOS M290). Further, the lab designed STWIP system is a coaxial high-speed (>10,000 fps) imaging system capable of monitoring MP temperature, morphology, and intensity profiles. The temperature measurements from STWIP are emissivity independent. The STWIP measured MP signatures of the printed tracks are correlated with the ex-situ microscopy characterized MP depth and the average grain lengths. From the data analysis, using support vector machine (SVM)-based regression models, we found that the MP temperature signatures are crucial for an accurate prediction of MP depth and the grain length, thus validating the novelty and necessity of the developed in-situ monitoring methods and analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents

Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their viscosities under both a range of environmental factors and formulations hinders their general application. While DESs may serve as designer solvents, with nearly unlimited combinations, this unfortunately makes it experimentally infeasible to comprehensively measure the viscosities of all DESs of potential industrial interest. To assist in the design of DESs, we have developed several new machine learning (ML) models that accurately and rapidly predict the viscosities of a diverse group of DESs at different temperatures and molar ratios using, to date, one of the most comprehensive data sets containing the properties of over 670 DESs over a wide range of temperatures (278.15–385.25 K). Three ML models, including support vector regression (SVR), feed forward neural networks (FFNNs), and categorical boosting (CatBoost), were developed to predict DES viscosity as a function of temperature and molar ratio and contrasted with multilinear and two-factor polynomial regression baselines. Further, quantum chemistry-based, COSMO-RS-derived sigma profile (σ-profile) features were used as inputs for the ML models. The CatBoost model is excellent at externally predicting DES viscosity, as indicated by high R 2 (0.99) and low root-mean-square-error (RMSE) and average absolute relative deviations (AARD) (5.22%) values for the testing data sets, and 98% of the data points lie within the 15% of AARD deviations. Furthermore, SHapley additive explanation (SHAP) analysis was employed to interpret the ML results and rationalize the viscosity predictions. The result is an ML approach that accurately predicts viscosity and will aid in accelerating the design of appropriate DESs for industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Neural speech recognition: continuous phoneme decoding using spatiotemporal representations of human cortical activity

The superior temporal gyrus (STG) and neighboring brain regions play a key role in human language processing. Previous studies have attempted to reconstruct speech information from brain activity in the STG, but few of them incorporate the probabilistic framework and engineering methodology used in modern speech recognition systems. Here, in this work, we describe the initial efforts toward the design of a neural speech recognition (NSR) system that performs continuous phoneme recognition on English stimuli with arbitrary vocabulary sizes using the high gamma band power of local field potentials in the STG and neighboring cortical areas obtained via electrocorticography. The system implements a Viterbi decoder that incorporates phoneme likelihood estimates from a linear discriminant analysis model and transition probabilities from an n-gram phonemic language model. Grid searches were used in an attempt to determine optimal parameterizations of the feature vectors and Viterbi decoder. The performance of the system was significantly improved by using spatiotemporal representations of the neural activity (as opposed to purely spatial representations) and by including language modeling and Viterbi decoding in the NSR system. These results emphasize the importance of modeling the temporal dynamics of neural responses when analyzing their variations with respect to varying stimuli and demonstrate that speech recognition techniques can be successfully leveraged when decoding speech from neural signals. Guided by the results detailed in this work, further development of the NSR system could have applications in the fields of automatic speech recognition and neural prosthetics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Far-from-equilibrium slow modes and momentum anisotropy in an expanding plasma

The momentum distribution of particle production in heavy-ion collisions encodes information about thermalization processes in the early-stage quark-gluon plasma. We use kinetic theory to study the far-from-equilibrium evolution of an expanding plasma with an anisotropic momentum-space distribution. We identify slow and fast degrees of freedom in the far-from-equilibrium plasma from the evolution of moments of this distribution. At late times, the slow modes correspond to hydrodynamic degrees of freedom and are naturally gapped from the fast modes by the inverse of the relaxation time, τ R − 1 . At early times, however, there are an infinite number of slow modes with a gap inversely proportional to time, τ − 1 . From the evolution of the slow modes we generalize the paradigm of the far-from-equilibrium attractor to vector and tensor components of the energy-momentum tensor, and even to higher moments of the distribution function that are not part of the hydrodynamic evolution. We predict that initial-state momentum anisotropy decays slowly in the far-from-equilibrium phase and may persist until the relaxation time. Published by the American Physical Society 2024

Brewer, Jasmine (ORCID:0000000230840663)↗

DOE OSTI2023

Urbanization may enhance tornado potential: A single case report

Tornadoes pose a risk of catastrophic economic loss and casualty in the United States. Modification of land use by urbanization alters the meteorological conditions that may impact tornado formation and intensification processes. Here we explored the simulated impact of Kansas City urbanization on the tornado potential of a supercell storm. In this studied case, we found that urbanization might enhance tornado potential by a) strengthening the low-level streamwise vorticity in the storm inflow region, thus forming stronger rotating updrafts; and b) intensifying near-surface horizontal vorticity near the boundary of the forward-flank cold pool which increases the ingestion, tilting, and stretching of streamwise horizontal vorticity into vertical vorticity. The former results from the stronger east-to-west pressure perturbation gradient due to the faster, stronger outflow boundary, and the latter is mainly a result of stronger cold fronts and a better alignment of storm-relative inflow with the horizontal vorticity vector. We emphasize that our conclusions only represent one possibility of how urbanization would affect tornado potential, and a more systematic examination is needed to achieve a more general conclusion.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Activation of AMPK by berberine induces hepatic lipid accumulation by upregulation of fatty acid translocase CD36 in mice

Emerging evidence has shown that berberine has a protective effect against metabolic syndrome such as obesity and type II diabetes mellitus by activating AMP-activated protein kinase (AMPK). AMPK induces CD36 trafficking to the sarcolemma for fatty acid uptake and oxidation in contracting muscle. However, little is known about the effects of AMPK on CD36 regulation in the liver. We investigated whether AMPK activation by berberine affects CD36 expression and fatty acid uptake in hepatocytes and whether it is linked to hepatic lipid accumulation. Activation of AMPK by berberine or transduction with adenoviral vectors encoding constitutively active AMPK in HepG2 and mouse primary hepatocytes increased the expression and membrane translocation of CD36, resulting in enhanced fatty acid uptake and lipid accumulation as determined by BODIPY-C16 and Nile red fluorescence, respectively. Activation of AMPK by berberine induced the phosphorylation of extracellular signal-regulated kinases 1/2 (ERK1/2) and subsequently induced CCAAT/enhancer-binding protein β (C/EBPβ) binding to the C/EBP-response element in the CD36 promoter in hepatocytes. In addition, hepatic CD36 expression and triglyceride levels were increased in normal diet-fed mice treated with berberine, but completely prevented when hepatic CD36 was silenced with adenovirus containing CD36-specific shRNA. Taken together, prolonged activation of AMPK by berberine increased CD36 expression in hepatocytes, resulting in fatty acid uptake via processes linked to hepatocellular lipid accumulation and fatty liver. - Highlights: • Berberine increases the expression and membrane translocation of CD36 in hepatocytes. • The increase of CD36 results in enhanced fatty acid uptake and lipid accumulation. • Berberine-induced fatty liver is mediated by AMPK-ERK-C/EBPβ pathway. • CD36-specific shRNA inhibited berberine-induced lipid accumulation in liver.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Optical spin hall effect in exciton–polariton condensates in lead halide perovskite microcavities

An exciton–polariton condensate is a hybrid light–matter state in the quantum fluid phase. The photonic component endows it with characters of spin, as represented by circular polarization. Spin-polarization can form stochastically for quasi-equilibrium exciton–polariton condensates at parallel momentum vector k|| ∼ 0 from bifurcation or deterministically for propagating condensates at k|| > 0 from the optical spin-Hall effect (OSHE). Here, we report deterministic spin-polarization in exciton–polariton condensates at k|| ∼ 0 in microcavities containing methylammonium lead bromide perovskite (CH3NH3PbBr3) single crystals under non-resonant and linearly polarized excitation. We observe two energetically split condensates with opposite circular polarizations and attribute this observation to the presence of strong birefringence, which introduces a large OSHE at k|| ∼ 0 and pins the condensates in a particular spin state. Such spin-polarized exciton–polariton condensates may serve not only as circularly polarized laser sources but also as effective alternatives to ultracold atom Bose–Einstein condensates in quantum simulators of many-body spin–orbit coupling processes.

Chemistry↗

DOE OSTI2017

Architecture Independent Integrated Early Performance and Energy Estimation

The end of Dennard’s scaling, coupled to the necessity to keep increasing computational performance in constrained power envelopes, is leading developers towards the need to opti- mize applications not only for performance, but also for energy consumption. In such a scenario, solutions that enable estimating performance and energy consumption of a program as early as possible, even during development and without the necessity to access the final target hardware, can become fundamental tools to reduce the design space, the optimization effort, and provide potential opportunities to automate the optimization process itself. In this position paper, we discuss the design of a performance and energy estimation framework based on a retargetable com- piler. Our proposed approach targets the Intermediate Repre- sentation (IR) of the LLVM compiler. The IR based approach enables, after a model is built, estimation from a host different from the target architecture, even considering dynamic infor- mation. We present the rationale behind such a framework, identify opportunities and components readily available (such as the provided static analysis, quick ways to add instrumentation for dynamic profiling, and the multiple backends), and aspects that still need further research efforts (such as more effective non-linear, or machine learning based models). We also discuss a hand-developed case study, based on a simple sparse matrix vector multiplication with a linear model, to motivate the needs for such a framework.

Estimation, Compilers, Performance Analysis↗