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DOE OSTI2020

Hydrodynamic and frictional modulation of deformations in switchable colloidal crystallites

Displacive transformations in colloidal crystals may offer a pathway for increasing the diversity of accessible configurations without the need to engineer particle shape or interaction complexity. To date, binary crystals composed of spherically symmetric particles at specific size ratios have been formed that exhibit floppiness and facile routes for transformation into more rigid structures that are otherwise not accessible by direct nucleation and growth. There is evidence that such transformations, at least at the micrometer scale, are kinetically influenced by concomitant solvent motion that effectively induces hydrodynamic correlations between particles. Here, we study quantitatively the impact of such interactions on the transformation of binary bcc-CsCl analog crystals into close-packed configurations. We first employ principal-component analysis to stratify the explorations of a bcc-CsCl crystallite into orthogonal directions according to displacement. We then compute diffusion coefficients along the different directions using several dynamical models and find that hydrodynamic correlations, depending on their range, can either enhance or dampen collective particle motions. These two distinct effects work synergistically to bias crystallite deformations toward a subset of the available outcomes.

42 ENGINEERING↗

DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

DOE OSTI2024

Unsupervised Learning for Improved Gamma-Ray Spectrometry in Pixelated Cadmium Zinc Telluride (CZT) Detectors

Machine learning has been found to be ubiquitously useful across many industries, presenting an opportunity to improve radiation detection performance using data-driven algorithms. Improved detector resolution can aid in the detection, identification, and quantification of radionuclides. Here, in this work, a novel, data-driven, unsupervised learning approach is developed to improve detector spectral characteristics by learning, and subsequently rejecting, poorly performing regions of the pixelated detector. Feature engineering is used to fit individual characteristic photo peaks to a Doniach lineshape with a linear background model. Then, principal component analysis is used to learn a lower-dimension latent space representation of each photo peak where the pixels are clustered, and subsequently ranked, based on the cluster mean distance to an optimal point. Pixels within the worst cluster(s) are rejected to improve the full-width at half-maximum (FWHM) by 10% to 15% (relative to the bulk detector) at 50% net efficiency when applied to training data obtained from measurements of a 100 μCi 154 Eu source using a H3D M400i pixelated cadmium zinc telluride detector. These results compare well with, but do not outperform, a greedy algorithm that accumulates pixels in order of FWHM from lowest to highest used as a benchmark. In the future, this approach can be extended to include the detector energy and angular response. Finally, the model is applied to newly seen natural and enriched uranium spectra relevant for nuclear safeguards applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Machine Learning–Augmented Laser-Induced Breakdown Spectroscopy for Spectral Discrimination of Iron Oxalates

Enhanced characterization and phase identification of post-PUREX Pu Oxalates (PuOXA) are pivotal for nonproliferation and pre-detonation nuclear forensics. Despite significant advances in the characterization of PuO 2 samples, little is known about the impact of both the chemical structure and oxidation states of PuOXA (i.e., Pu(III) and Pu(IV)) have on optical emission signatures. Here, we demonstrate the analytical capabilities of laser-induced breakdown spectroscopy (LIBS) applied to Fe(II) and Fe(III) oxalate samples as surrogates for PuOXA, highlighting the discriminating features in the LIBS emission spectra arising from differences in the oxidation states within mixed FeOXA samples. We report the enhancement of spectral feature selection using Principal Component Analysis (PCA), which enables the analytical superiority of machine learning algorithms such as Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA), Partial Least Squares Regression (PLSR), Support Vector Regression (SVR), and Random Forest Regression (RFR) over conventional univariate techniques for phase discrimination and chemometric analysis. Cluster analysis revealed how both matrix effects and laser ablation influence cluster separability by introducing spectral artifacts that misdirect the maximization of variance. PCA-selected emission lines were used in the regression models, demonstrating that both univariate and multivariate linear regression models (i.e., PLSR and SVR) can achieve acceptable performance, with machine learning models outperforming conventional calibration regressions. Furthermore, the application of non-linearly activated PCA-selected emission lines illustrates how simplifying the data while retaining captured variance enables the use of less complex and more computationally efficient models. Furthermore, this is particularly evident in the underperformance of RFR, which suffers from increased computational costs and overfitting owing to its high complexity.

Oxalates↗

DOE OSTI2020

Tracking atomic structure evolution during directed electron beam induced Si-atom motion in graphene via deep machine learning

Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. Here, the analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

A 28 nm multiply-accumulate ASIC architecture for on-chip data compression in MHz frame rate X-ray and electron pixel detectors

Modern X-ray detector systems urgently require compact, efficient, and fast data compression schemes to handle the transmission of big data from pixel arrays, enabling frame rates in the MHz regime. Here, in this work, a data compression ASIC that implements a streaming fixed-length lossy compression scheme is introduced and analyzed, proving the feasibility and benefits of on-chip compression. The compression scheme utilizes a vector matrix product logic, which performs a number of floating-point multiplications, additions, and accumulations. The logic is verified, synthesized, and shown to fit in the area resource available for the X-ray detector under study, which comprises 192 × 168 pixels each of 12-bit width, and having a total area of 20 mm× 20 mm, about 2 mm× 20 mm of which are available for the digital logic. Several system architectures, precisions, and compression ratios ranging from 100 to 250 were analyzed to pave the way for on-chip fixed-length compression (e.g., principal component analysis, singular value decomposition) and data reduction (e.g., azimuthal integration) for X-ray and electron detectors.

Data compression↗

DOE OSTI2024

Towards revealing intrinsic vortex-core states in Fe-based superconductors through statistical discovery

Abstract In type-II superconductors, electronic states within magnetic vortices hold crucial information about the paring mechanism and can reveal non-trivial topology. While scanning tunneling microscopy/spectroscopy (STM/S) is a powerful tool for imaging superconducting vortices, it is challenging to isolate the intrinsic electronic properties from extrinsic effects like subsurface defects and disorders. Here we combine STM/STS with basic machine learning to develop a method for screening out the vortices pinned by embedded disorder in iron-based superconductors. Through a principal component analysis of large STS data within vortices, we find that the vortex-core states in Ba(Fe 0.96 Ni 0.04 ) 2 As 2 start to split into two categories at certain magnetic field strengths, reflecting vortices with and without pinning by subsurface defects or disorders. Our machine-learning analysis provides an unbiased approach to reveal intrinsic vortex-core states in novel superconductors and shed light on ongoing puzzles in the possible emergence of a Majorana zero mode.

Guo, Yueming↗

DOE OSTI2021

An end-to-end trainable hybrid classical-quantum classifier

Abstract We introduce a hybrid model combining a quantum-inspired tensor network and a variational quantum circuit to perform supervised learning tasks. This architecture allows for the classical and quantum parts of the model to be trained simultaneously, providing an end-to-end training framework. We show that compared to the principal component analysis, a tensor network based on the matrix product state with low bond dimensions performs better as a feature extractor for the input data of the variational quantum circuit in the binary and ternary classification of MNIST and Fashion-MNIST datasets. The architecture is highly adaptable and the classical-quantum boundary can be adjusted according to the availability of the quantum resource by exploiting the correspondence between tensor networks and quantum circuits.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Abstract Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

Environmental Sciences & Ecology↗

DOE OSTI2023

The influence of physical and algorithmic factors on simulated far-field waveforms and source–time functions of underground explosions using unsupervised machine learning

SUMMARY Characterizing explosion sources and differentiating between earthquake and underground explosions using distributed seismic networks becomes non-trivial when explosions are detonated in cavities or heterogeneous ground material. Moreover, there is little understanding of how changes in subsurface physical properties affect the far-field waveforms we record and use to infer information about the source. Simulations of underground explosions and the resultant ground motions can be a powerful tool to systematically explore how different subsurface properties affect far-field waveform features, but there are added variables that arise from how we choose to model the explosions that can confound interpretation. To assess how both subsurface properties and algorithmic choices affect the seismic wavefield and the estimated source functions, we ran a series of 2-D axisymmetric non-linear numerical explosion experiments and wave propagation simulations that explore a wide array of parameters. We then inverted the synthetic far-field waveform data using a linear inversion scheme to estimate source–time functions (STFs) for each simulation case. We applied principal component analysis (PCA), an unsupervised machine learning method, to both the far-field waveforms and STFs to identify the most important factors that control variance in the waveform data and differences between cases. For the far-field waveforms, the largest variance occurs in the shallower radial receiver channels in the 0–50 Hz frequency band. For the STFs, both peak amplitude and rise times across different frequencies contribute to the variance. We find that the ground equation of state (i.e. lithology and rheology) and the explosion emplacement conditions (i.e. tamped versus cavity) have the greatest effect on the variance of the far-field waveforms and STFs, with the ground yield strength and fracture pressure being secondary factors. Differences in the PCA results between the far-field waveforms and STFs could possibly be due to near-field non-linearities of the source that are not accounted for in the estimation of STFs and could be associated with yield strength, fracture pressure, cavity radius and cavity shape parameters. Other algorithmic parameters are found to be less important and cause less variance in both the far-field waveforms and STFs, meaning algorithmic choices in how we model explosions are less important, which is encouraging for the further use of explosion simulations to study how physical Earth properties affect seismic waveform features and estimated STFs.

58 GEOSCIENCES↗

DOE OSTI2020

Surrogate modelling the Baryonic Universe – I. The colour of star formation

The spectral energy distribution of a galaxy emerges from the complex interplay of many physical ingredients, including its star formation history (SFH), metallicity evolution, and dust properties. Using GALAXPY , a new galaxy spectral prediction tool, and SFHs predicted by the empirical model UNIVERSEMACHINE and the cosmological hydrodynamical simulation IllustrisTNG, we isolate the influence of SFH on optical and near-infrared colours from 320 to 1080 Å at z = 0. By carrying out a principal component analysis, we demonstrate that physically motivated SFH variations modify galaxy colours along a single direction in colour space: the SFH-direction. We find that the projection of a galaxy’s present-day colours on to the SFH-direction is almost completely regulated by the fraction of stellar mass that the galaxy formed over the last billion years. Together with cosmic downsizing, this results in galaxies becoming redder as their host halo mass increases. We additionally study the change in galaxy colours due to variations in metallicity, dust attenuation, and nebular emission lines, finding that these properties vary broad-band colours along distinct directions in colour space relative to the SFH-direction. Finally, we show that the colours of low-redshift Sloan Digital Sky Survey galaxies span an ellipsoid with significant extent along two independent dimensions, and that the SFH-direction is well-aligned with the major axis of this ellipsoid. Our analysis supports the conclusion that variations in SFH are the dominant influence on present-day galaxy colours, and that the nature of this influence is strikingly simple.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Non-Gaussianity in the weak lensing correlation function likelihood – implications for cosmological parameter biases

ABSTRACT We study the significance of non-Gaussianity in the likelihood of weak lensing shear two-point correlation functions, detecting significantly non-zero skewness and kurtosis in 1D marginal distributions of shear two-point correlation functions in simulated weak lensing data. We examine the implications in the context of future surveys, in particular LSST, with derivations of how the non-Gaussianity scales with survey area. We show that there is no significant bias in 1D posteriors of Ωm and σ8 due to the non-Gaussian likelihood distributions of shear correlations functions using the mock data (100 deg2). We also present a systematic approach to constructing approximate multivariate likelihoods with 1D parametric functions by assuming independence or more flexible non-parametric multivariate methods after decorrelating the data points using principal component analysis (PCA). While the use of PCA does not modify the non-Gaussianity of the multivariate likelihood, we find empirically that the 1D marginal sampling distributions of the PCA components exhibit less skewness and kurtosis than the original shear correlation functions. Modelling the likelihood with marginal parametric functions based on the assumption of independence between PCA components thus gives a lower limit for the biases. We further demonstrate that the difference in cosmological parameter constraints between the multivariate Gaussian likelihood model and more complex non-Gaussian likelihood models would be even smaller for an LSST-like survey. In addition, the PCA approach automatically serves as a data compression method, enabling the retention of the majority of the cosmological information while reducing the dimensionality of the data vector by a factor of ∼5.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Reionization history constraints from neural network based predictions of high-redshift quasar continua

ABSTRACT Observations of the early Universe suggest that reionization was complete by z ∼ 6, however, the exact history of this process is still unknown. One method for measuring the evolution of the neutral fraction throughout this epoch is via observing the Lyα damping wings of high-redshift quasars. In order to constrain the neutral fraction from quasar observations, one needs an accurate model of the quasar spectrum around Lyα, after the spectrum has been processed by its host galaxy but before it is altered by absorption and damping in the intervening intergalactic medium (IGM). In this paper, we present a novel machine learning approach, using artificial neural networks, to reconstruct quasar continua around Lyα. Our Quasar Spectra from Artificial Neural Network based predictive Regression Algorithm(QSANNdRA) improves the error in this reconstruction compared to the state-of-the-art principal component analysis (PCA) based model in the literature by 14.2 per cent on average, and provides an improvement of 6.1 per cent on average when compared to an extension thereof. In comparison with the extended PCA model, QSANNdRA further achieves an improvement of 22.1 per cent and 16.8 per cent when evaluated on low-redshift quasars most similar to the two high-redshift quasars under consideration, ULAS J1120+0641 at z = 7.0851 and ULAS J1342+0928 at z = 7.5413, respectively. Using our more accurate reconstructions of these two z > 7 quasars, we estimate the neutral fraction of the IGM using a homogeneous reionization model and find $\bar{x}_\mathrm{H\, \small{I}} = 0.25^{+0.05}_{-0.05}$ at z = 7.0851 and $\bar{x}_\mathrm{H\, \small{I}} = 0.60^{+0.11}_{-0.11}$ at z = 7.5413. Our results are consistent with the literature and favour a rapid end to reionization.

Ďurovčíková, Dominika↗

DOE OSTI2021

Surrogate modelling the Baryonic Universe II: On forward modelling the colours of individual and populations of galaxies

ABSTRACT Among the properties shaping the light of a galaxy, the star formation history (SFH) is one of the most challenging to model due to the variety of correlated physical processes regulating star formation. In this work, we leverage the stellar population synthesis model fsps, together with SFHs predicted by the hydrodynamical simulation IllustrisTNG and the empirical model universemachine, to study the impact of star formation variability on galaxy colours. We start by introducing a model-independent metric to quantify the burstiness of a galaxy formation model, and we use this metric to demonstrate that universemachine predicts SFHs with more burstiness relative to IllustrisTNG. Using this metric and principal component analysis, we construct families of SFH models with adjustable variability, and we show that the precision of broad-band optical and near-infrared colours degrades as the level of unresolved short-term variability increases. We use the same technique to demonstrate that variability in metallicity and dust attenuation presents a practically negligible impact on colours relative to star formation variability. We additionally provide a model-independent fitting function capturing how the level of unresolved star formation variability translates into imprecision in predictions for galaxy colours; our fitting function can be used to determine the minimal SFH model that reproduces colours with some target precision. Finally, we show that modelling the colours of individual galaxies with per cent-level precision demands resorting to complex SFH models, while producing precise colours for galaxy populations can be achieved using models with just a few degrees of freedom.

Chaves-Montero, Jonás (ORCID:0000000295534261)↗

DOE OSTI2023

Exploring the dependence of gas cooling and heating functions on the incident radiation field with machine learning

ABSTRACT Gas cooling and heating functions play a crucial role in galaxy formation. But, it is computationally expensive to exactly compute these functions in the presence of an incident radiation field. These computations can be greatly sped up by using interpolation tables of pre-computed values, at the expense of making significant and sometimes even unjustified approximations. Here, we explore the capacity of machine learning to approximate cooling and heating functions with a generalized radiation field. Specifically, we use the machine learning algorithm XGBoost to predict cooling and heating functions calculated with the photoionization code cloudy at fixed metallicity, using different combinations of photoionization rates as features. We perform a constrained quadratic fit in metallicity to enable a fair comparison with traditional interpolation methods at arbitrary metallicity. We consider the relative importance of various photoionization rates through both a principal component analysis (PCA) and calculation of SHapley Additive exPlanation (shap) values for our XGBoost models. We use feature importance information to select different subsets of rates to use in model training. Our XGBoost models outperform a traditional interpolation approach at each fixed metallicity, regardless of feature selection. At arbitrary metallicity, we are able to reduce the frequency of the largest cooling and heating function errors compared to an interpolation table. We find that the primary bottleneck to increasing accuracy lies in accurately capturing the metallicity dependence. This study demonstrates the potential of machine learning methods such as XGBoost to capture the non-linear behaviour of cooling and heating functions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Detecting anomalous SRF cavity behavior with unsupervised learning

We present an unsupervised learning framework for detecting anomalous superconducting radio-frequency (SRF) cavity behavior at the Continuous Electron Beam Accelerator Facility (CEBAF), emphasizing its initial performance and effectiveness. Key to the system’s success was the development of data acquisition systems (DAQs) that capture fast-sampled, information-rich signals, essential for detecting transient effects. The approach involves creating daily cavity-specific models using principal component analysis to handle variations in rf signal behavior and mitigate performance degradation from data drift. This unsupervised method eliminates the need for expensive labeling by continuously updating models with recent data. Deployed and operational for 3 months before a scheduled shutdown, the system successfully identified several issues with DAQ signals, confirming its effectiveness. Despite access to only a fraction of CEBAF’s SRF cavity signals, the framework efficiently detected several instances requiring intervention, demonstrating a significant improvement over traditional, labor-intensive methods of manual plot inspection. Published by the American Physical Society 2025

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Statistical tools for a better optical model

Background: Modern statistical tools provide the ability to compare the information content of observables and provide a path to explore which experiments would be most useful to give insight into and constrain theoretical models. Purpose: Here we study three such tools in the context of nuclear reactions with the goal of constraining the optical potential. Method: The three statistical tools examined are (i) the principal component analysis, (ii) the sensitivity analysis based on derivatives, and (iii) the Bayesian evidence. We first apply these tools to a toy-model case, comparing the form of the imaginary part of the optical potential. Then we consider two different reaction observables, elastic angular distributions and polarization data for reactions on 48 Ca and 208 Pb at two different beam energies. Results: For the toy-model case, we find significant discrimination power in the sensitivities and the Bayesian evidence, showing clearly that the volume imaginary term is more useful to describe scattering at higher energies. When comparing between elastic cross sections and polarization data using realistic optical models, sensitivity studies indicate that both observables are roughly equally sensitive but the variability of the optical model parameters is strongly angle dependent. The Bayesian evidence shows some variability between the two observables, but the Bayes factor obtained is not sufficient to discriminate between angular distributions and polarization. Conclusions: From the cases considered, we conclude that, in general, elastic scattering angular distributions have similar impact in constraining the optical potential parameters compared with the polarization data. The angular ranges for the optimum experimental constraints can vary significantly with the observable considered.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Training and projecting: A reduced basis method emulator for many-body physics

Here, we present the reduced basis method as a tool for developing emulators for equations with tun able parameters within the context of the nuclear many-body problem. The method uses a basis expansion informed by a set of solutions for a few values of the model parameters and then projects the equations over a well-chosen low-dimensional subspace. We connect some of the results in the eigenvector continuation literature to the formalism of reduced basis methods and show how these methods can be applied to a broad set of problems. As we illustrate, the possible success of the formalism on such problems can be diagnosed beforehand by a principal component analysis. We apply the reduced basis method to the one-dimensional Gross-Pitaevskii equation with a harmonic trap ping potential and to nuclear density functional theory for 48 Ca, achieving speed-ups of more than x150 and x250, respectively, when compared to traditional solvers. The outstanding performance of the approach, together with its straightforward implementation, show promise for its application to the emulation of computationally demanding calculations, including uncertainty quantification.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗