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DOE OSTI2023

Bridging the Gap between Cosmological Simulations with Graph Neural Networks and Domain Adaptation

Deep learning models have been shown to outperform methods that rely on summary statistics, like the power spectrum, in extracting information from complex cosmological data sets. However, due to differences in the subgrid physics implementation and numerical approximations across different simulation suites, models trained on data from one cosmological simulation show a drop in performance when tested on another. Similarly, models trained on any of the simulations would also likely experience a drop in performance when applied to observational data. Training on data from two different suites of the CAMELS hydrodynamic cosmological simulations, we examine the generalization capabilities of Domain Adaptive Graph Neural Networks (DA-GNNs). By utilizing GNNs, we capitalize on their capacity to capture structured scale-free cosmological information from galaxy distributions. Moreover, by including unsupervised domain adaptation via Maximum Mean Discrepancy (MMD), we enable our models to extract domain-invariant features. We demonstrate that DA-GNN achieves higher accuracy and robustness on cross dataset tasks (up to 28% better relative error and up to almost an order of magnitude better χ 2 ). Using data visualizations, we show the effects of domain adaptation on proper latent space data alignment. This shows that DA-GNNs are a promising method for extracting domain-independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Domain Adaptive Graph Neural Networks for Constraining Cosmological Parameters Across Multiple Data Sets

Deep learning models have been shown to outperform methods that rely on summary statistics, like the power spectrum, in extracting information from complex cosmological data sets. However, due to differences in the subgrid physics implementation and numerical approximations across different simulation suites, models trained on data from one cosmological simulation show a drop in performance when tested on another. Similarly, models trained on any of the simulations would also likely experience a drop in performance when applied to observational data. Training on data from two different suites of the CAMELS hydrodynamic cosmological simulations, we examine the generalization capabilities of Domain Adaptive Graph Neural Networks (DA-GNNs). By utilizing GNNs, we capitalize on their capacity to capture structured scale-free cosmological information from galaxy distributions. Moreover, by including unsupervised domain adaptation via Maximum Mean Discrepancy (MMD), we enable our models to extract domain-invariant features. We demonstrate that DA-GNN achieves higher accuracy and robustness on cross-dataset tasks (up to $28\%$ better relative error and up to almost an order of magnitude better $\chi^2$). Using data visualizations, we show the effects of domain adaptation on proper latent space data alignment. This shows that DA-GNNs are a promising method for extracting domain-independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

An adaptive adversarial domain adaptation approach for corn yield prediction

Recently, statistical machine learning and deep learning methods have been widely explored for corn yield prediction. Though successful, machine learning models generated within a specific spatial domain often lose their validity when directly applied to new regions. To address this issue, we designed an unsupervised adaptive domain adversarial neural network (ADANN). Specifically, through domain adversarial training, the ADANN model reduced the impact of domain shift by projecting data from different domains into the same subspace. Also, the ADANN model was designed to be trained in an adaptive way, which guaranteed the model can learn the domain-invariant features and perform accurate yield prediction simultaneously. Informative variables including time-series vegetation indices and sequential weather observations were first collected from multiple data sources and aggregated to the county level. Then, we trained the ADANN model with the extracted features and corresponding reported county-level corn yield from the U.S. Department of Agriculture (USDA). Finally, the trained model was evaluated in four testing years 2016–2019. The U.S. corn belt was used as the study area and counties under study were grouped into two diverse ecological regions. Overall, the experimental results showed that the developed ADANN model had better performance than three other state-of-the-art machine learning models in both local experiments (train and test in the same region) and transfer experiments (train and test in different regions). As the first study using adversarial learning for crop yield prediction, this research demonstrates a novel solution for improving model transferability on crop yield prediction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

State of the Art in Time‐Dependent Flow Topology: Interpreting Physical Meaningfulness Through Mathematical Properties

Abstract We present a state‐of‐the‐art report on time‐dependent flow topology. We survey representative papers in visualization and provide a taxonomy of existing approaches that generalize flow topology from time‐independent to time‐dependent settings. The approaches are classified based upon four categories: tracking of steady topology, reference frame adaption, pathline classification or clustering, and generalization of critical points. Our unique contributions include introducing a set of desirable mathematical properties to interpret physical meaningfulness for time‐dependent flow visualization, inferring mathematical properties associated with selective research papers, and utilizing such properties for classification. The five most important properties identified in the existing literature include coincidence with the steady case, induction of a partition within the domain, Lagrangian invariance, objectivity, and Galilean invariance.

Bujack, Roxana↗

DOE OSTI2020

High‐order symmetric cubature rules for tetrahedra and pyramids

Abstract In this article, we present an algorithm to construct high‐order fully symmetric cubature rules for tetrahedral and pyramidal elements, with positive weights and integration points that are in the interior of the domain. Cubature rules are fully symmetric if they are invariant to affine transformations of the domain. We divide the integration points into symmetry orbits where each orbit contains all the points generated by the permutation stars. These relations are represented by equality constraints. The construction of symmetric cubature rules require the solution of nonlinear polynomial equations with both inequality and equality constraints. For higher orders, we use an algorithm that consists of five sequential phases to produce the cubature rules. In the literature, symmetric numerical integration rules are available for the tetrahedron for orders p = 1 – 10, 14 , and for the pyramid up to p = 10 . We have obtained fully symmetric cubature rules for both of these elements up to order p = 20 . Numerical tests are presented that verify the polynomial‐precision of the cubature rules. Convergence studies are performed for the integration of exponential, weakly singular, and trigonometric test functions over both elements with flat and curved faces. With increase in p , improvements in accuracy is realized, though nonmonotonic convergence is observed.

Jaśkowiec, Jan↗

DOE OSTI2021

Disentangling ferroelectric domain wall geometries and pathways in dynamic piezoresponse force microscopy via unsupervised machine learning

In this work, domain switching pathways in ferroelectric materials visualized by dynamic piezoresponse force microscopy (PFM) are explored via variational autoencoder, which simplifies the elements of the observed domain structure, crucially allowing for rotational invariance, thereby reducing the variability of local polarization distributions to a small number of latent variables. For small sampling window sizes the latent space is degenerate, and variability is observed only in the direction of a single latent variable that can be identified with the presence of domain wall. For larger window sizes, the latent space is 2D, and the disentangled latent variables can be generally interpreted as the degree of switching and complexity of domain structure. Applied to multiple consecutive PFM images acquired while monitoring domain switching, the polarization switching mechanism can thus be visualized in the latent space, providing insight into domain evolution mechanisms and their correlation with the microstructure.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Disentangling Ferroelectric Wall Dynamics and Identification of Pinning Mechanisms via Deep Learning

Field-induced domain-wall dynamics in ferroelectric materials underpins multiple applications ranging from actuators to information technology devices and necessitates a quantitative description of the associated mechanisms including giant electromechanical couplings, controlled nonlinearities, or low coercive voltages. While the advances in dynamic piezoresponse force microscopy measurements over the last two decades have rendered visualization of polarization dynamics relatively straightforward, the associated insights into the local mechanisms have been elusive. This work explores the domain dynamics in model polycrystalline materials using a workflow combining deep-learning-based segmentation of the domain structures with nonlinear dimensionality reduction using multilayer rotationally invariant autoencoders (rVAE). The former allows unambiguous identification and classification of the ferroelectric and ferroelastic domain walls. Here, the rVAE discovers the latent representations of the domain wall geometries and their dynamics, consequently providing insight into the intrinsic mechanisms of polarization switching, that can further be compared to simple physical models. The rVAE disentangles the factors affecting the pinning efficiency of ferroelectric walls, offering insights into the correlation of ferroelastic wall distribution and ferroelectric wall pinning.

36 MATERIALS SCIENCE↗

DOE OSTI2025

RINO: Renormalization Group Invariance with No Labels

A common challenge with supervised machine learning (ML) in high energy physics (HEP) is the reliance on simulations for labeled data, which can often mismodel the underlying collision or detector response. To help mitigate this problem of domain shift, we propose RINO (Renormalization Group Invariance with No Labels), a self-supervised learning approach that can instead pretrain models directly on collision data, learning embeddings invariant to renormalization group flow scales. In this work, we pretrain a transformer-based model on jets originating from quantum chromodynamic (QCD) interactions from the JetClass dataset, emulating real QCD-dominated experimental data, and then finetune on the JetNet dataset -- emulating simulations -- for the task of identifying jets originating from top quark decays. RINO demonstrates improved generalization from the JetNet training data to JetClass data compared to supervised training on JetNet from scratch, demonstrating the potential for RINO pretraining on real collision data followed by fine-tuning on small, high-quality MC datasets, to improve the robustness of ML models in HEP.

Hao, Zichun [Caltech] (ORCID:0000000256244907)↗

DOE OSTI2022

The Bouger's Law Shell Ionospheric Transfer Function

Ionospheric transfer function (ITF) algorithms determine the effects of the ionosphere on an electromagnetic (EM) radio-frequency (RF) signal as it propagates through. In this report, the Bouger’s law shell model is outlined. This ITF is very similar to the Snell’s Law Shell ITF; however, in this formulation, plasma parameters in the ionosphere are allowed to change radially. This algorithm is expressed in the frequency domain. In this way, it is applied as linear time invariant (LTI) filter function. Signals in this report are assumed to have only a single component (i.e. x, y or z in a rectangular coordinate system). Multi-component signals can be treated simply by applying the specific ITF to each component separately.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Stability Analysis of Parameter Varying Genetic Toggle Switches Using Koopman Operators

The genetic toggle switch is a well known model in synthetic biology that represents the dynamic interactions between two genes that repress each other. The mathematical models for the genetic toggle switch that currently exist have been useful in describing circuit dynamics in rapidly dividing cells, assuming fixed or time-invariant kinetic rates. There is a growing interest in being able to model and extend synthetic biological function for growth conditions such as stationary phase or during nutrient starvation. As cells transition from one growth phase to another, kinetic rates become time-varying parameters. In this paper, we propose a novel class of parameter varying nonlinear models that can be used to describe the dynamics of genetic circuits, including the toggle switch, as they transition from different phases of growth. We show that there exists unique solutions for this class of systems, as well as for a class of systems that incorporates the microbial phenomena of quorum sensing. Further, we show that the domain of these systems, which is the positive orthant, is positively invariant. We also showcase a theoretical control strategy for these systems that would grant asymptotic monostability of a desired fixed point. We then take the general form of these systems and analyze their stability properties through the framework of time-varying Koopman operator theory. A necessary condition for asymptotic stability is also provided as well as a sufficient condition for instability. A Koopman control strategy for the system is also proposed, as well as an analogous discrete time-varying Koopman framework for applications with regularly sampled measurements.

Harrison, Jamiree (ORCID:0000000265351579)↗

DOE OSTI2023

Ferrorotational domain walls revealed by electric quadrupole second harmonic generation microscopy

Domain walls are ubiquitous in materials that undergo phase transitions driven by spontaneous symmetry breaking. Domain walls in ferroics and multiferroics have received tremendous attention recently due to their emergent properties distinct from their domain counterparts—for example, their high mobility and controllability, as well as their potential applications in nanoelectronics. However, it is extremely challenging to detect, visualize, and study the ferrorotational (FR) domain walls because the FR order, in contrast to ferromagnetism and ferroelectricity, is invariant under both the spatial-inversion and the time-reversal operations and, thus, hardly couple with conventional experimental probes. Here, a FR candidate NiTi⁢O 3 is investigated by ultrasensitive electric quadrupole (EQ) second-harmonic generation rotational anisotropy (SHG RA) to probe the point symmetries of the two degenerate FR domain states, showing their relation by the vertical mirror operations that are broken below the FR critical temperature. We then visualize the real-space FR domains by scanning EQ SHG microscopy, and further, resolve the FR domain walls by revealing a suppressed SHG intensity at the domain walls. By taking local EQ SHG RA measurements, we show the restoration of the mirror symmetry at FR domain walls and prove their unconventional nonpolar nature. In conclusion, our findings not only provide a comprehensive insight into FR domain walls, but also demonstrate a unique and powerful tool for future studies on domain walls of unconventional ferroics both of which pave the way towards future manipulations and applications of FR domain walls.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Various Low-Symmetry Phases in High- χ and Conformationally Asymmetric PDMS- b -PTFEA Copolymers

Since the discovery of the Frank–Kasper (FK) phase a decade ago, single-component block copolymer systems have offered unique opportunities to explore the structural and phase-transition properties of topologically close-packed FK phases composed of point-particle motifs. Here, we present the formation of complex low-symmetry phases and their thermodynamic stability using high-χ and high-ε linear diblock copolymers, where χ and ε are the Flory–Huggins interaction parameter and conformational asymmetry between the two blocks, respectively. In this work, a series of polydimethylsiloxane-b-poly(2,2,2-trifluoroethyl acrylate) (PDMS-b-PTFEA) copolymers are prepared by tuning the volume fraction ($f_{\text{PTFEA}}$) of a minor PTFEA block. The packing structures of PDMS-b-PTFEAs are mapped in the space of temperature versus $f_{\text{PTFEA}}$ using X-ray scattering measurements. In addition to the packing structures reported earlier, we identify another A15 phase at higher $f_{\text{PTFEA}}$ close to a hexagonally packed cylinder (HEX) phase and establish the phase sequence of HEX–A15–σ–C14–BCC with decreasing $f_{\text{PTFEA}}$. Theoretical calculation of relative free-energy densities confirms the experimental phase sequence of the composition-dependent sphere-packing structures. Interestingly, the domain sizes of three-dimensional (3D) sphere-packing structures are nearly temperature-invariant compared to that of a two-dimensional HEX structure, and we attribute this dimensional stability to the strong enthalpic effects in the formation of 3D packing structures and the geometrical characteristics of spherical domains. Our results demonstrate that the interaction parameter χ, together with the known role of conformational asymmetry ε, serves as the primary thermodynamic parameter for selecting and stabilizing various low-symmetry packing structures in sphere-forming linear diblock copolymer systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Reconstruction of decays to merged photons using end-to-end deep learning with domain continuation in the CMS detector

A novel technique based on machine learning is introduced to reconstruct the decays of highly Lorentz-boosted particles. Using an end-to-end deep learning strategy, the technique bypasses existing rule-based particle reconstruction methods typically used in high energy physics analyses. It uses minimally processed detector data as input and directly outputs particle properties of interest. The new technique is demonstrated for the reconstruction of the invariant mass of particles decaying in the CMS detector. The decay of a hypothetical scalar particle A into two photons, A → γ γ , is chosen as a benchmark decay. Lorentz boosts γ L = 60 – 600 are considered, ranging from regimes where both photons are resolved to those where the photons are closely merged as one object. A training method using domain continuation is introduced, enabling the invariant mass reconstruction of unresolved photon pairs in a novel way. The new technique is validated using π 0 → γ γ decays in LHC collision data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

The influence of cooling rates on strain phase diagrams and domain structures of ferroelectric thin films: A case study of PbTiO 3

Strain engineering has been established as an effective approach to control phase equilibria, domain configurations, and functional properties of ferroelectric thin films. Temperature-strain phase diagrams have been used as powerful tools for providing insights into strain engineering. However, almost all existing phase diagrams established using the phase-field approach assume quenching conditions without considering actual cooling rates during the post-deposition annealing process of ferroelectric thin films. Within this work, we systematically investigate the influence of cooling rates on domain structures and the strain-phase diagram of ferroelectric thin films using phase-field simulations, taking PbTiO 3 thin films as a model system. We found that both the position of phase boundaries in the strain phase diagrams and the domain morphology are significantly influenced by the cooling rates. It is revealed that while the paraelectric-ferroelectric phase boundary remains invariant, the phase boundaries between single-phase and multi-phase regions tend to shift toward the corresponding multi-phase region as the cool rate reduces. Slow cooling generally leads to more ordered domain structures with increased domain size. Using the obtained equilibrium domain structures, we calculated effective thermal conductivities and found significant variations that can be tuned by the cooling rates. In conclusion, this work reveals an underexplored yet critical impact of cooling rates on phase equilibria and domain structures in ferroelectric thin films, which may inspire further fine-tuning of domains and domain walls in low-dimensional ferroelectrics for multifunctional applications.

Domain structures↗

DOE OSTI2021

Gauge invariance and Ward identities in nonlinear response theory

We present a formal analysis of nonlinear response functions in terms of correlation functions in real- and imaginary-time domains. In particular, we show that causal nonlinear response functions, expressed in terms of nested commutators in real time, can be obtained from the analytic continuation of time-ordered response functions, which are more easily amenable to diagrammatic calculation. This generalizes the well-known result of linear response theory. We then use gauge invariance arguments to derive exact relations between second-order response functions in density and current channels. These identities, which are non-perturbative in the strength of inter-particle interactions, allow us to establish exact connections between nonlinear optics calculations done in different electromagnetic gauges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗

DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

DOE OSTI2026

Composite-dimensional topological codes with boundaries and defects

We introduce new algorithms and provide example constructions of stabilizer models for the gapped boundaries, domain walls, and 0D defects of Abelian composite-dimensional twisted quantum doubles. Using the physically intuitive concept of condensation, our algorithm explicitly describes how to construct the boundary and domain-wall stabilizers starting from the bulk model. This extends the utility of Pauli stabilizer models in describing nontranslationally invariant topological orders with gapped boundaries. To highlight this utility, we provide a series of examples, including a new family of quantum error-correcting codes where the double of ℤ4 is coupled to instances of the double semion (DS) phase. We discuss the codes' utility in the burgeoning area of quantum error correction with an emphasis on the interplay between deconfined anyons, logical operators, error rates, and decoding. We also augment our construction, built using algorithmic tools to describe the properties of explicit stabilizer layouts at the microscopic lattice level, with dimensional counting arguments and macroscopic-level constructions building on pants decompositions. The latter outlines how such codes' representation and design can be automated. Our results are validated by a series of error-correcting threshold calculations comparing our codes' performance with that of standard surface codes. To do so, we introduce a composite-dimensional belief-propagation decoder with ordered statistics that utilizes combination sweeps. Going beyond our worked-out examples, we expect our explicit step-by-step algorithms to pave the path for higher-dimensional codes to be discovered and implemented in near-future architectures that take advantage of various hardware platforms.

Mousa, Mohamad [Purdue University]↗