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At least 19 records

Affine Transformations to Correlate Experimental and Simulated EDS Spectra for Multi-Element Systems

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Computing the Critical Temperature of the Affine-Transformed $D=3$ Ising Model Using Masked Autoregressive Flow

The simple Ising model provides a rich environment to build and study lattice field theories. As part of an ongoing project to construct a conformal field theory (CFT) on an arbitrarily curved manifold, in this work we develop methods to measure the critical temperature $β_c$ of the affine-transformed Ising model on the face-centered cubic (FCC) lattice. The main challenge in this endeavor is finding a computationally efficient and accurate method of interpolating and extrapolating Monte Carlo observables with respect to coupling coefficients and temperature. Herein, we compare two such methods. A traditional statistical approach uses the multiple histogram (MH) method, while a newer machine learning approach uses a masked autoregressive flow (MAF) to estimate the underlying probability density function of a set of observables. While the MH method is specifically designed to interpolate and extrapolate Monte Carlo observables, we find that MAF is a viable alternative for measuring $β_c$ with a computational cost that scales more favorably. Furthermore, we comment on additional advantages of MAF relevant to our work, such as extrapolating in system volume.

Svenson, Kai [Texas U.]↗

Affine Transformations to Enable Machine Learning for Semi-Quantitative EDS Analysis

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Energy-momentum tensor in the 2D Ising CFT in full modular space

A set of lattice operators for the energy-momentum (EM) tensor in the Ising CFT is derived in the spin variables. Our expression works under arbitrary affine transformation both on triangular and hexagonal lattices (where the former includes the rectangular lattices). The correctness of the operators is numerically confirmed in Monte Carlo calculations by comparing the results with the conformal Ward identity, including the operator normalization. In the derivation of the EM tensor, a staggered structure of the affine-transformed hexagonal lattice is analyzed, which shows a peculiar shift from the circumcenter dual lattice and appears as a mixing angle between the holomorphic part $T(z)$ and the antiholomorphic part $\tilde T(\bar z)$. The details of this contribution will appear in a subsequent paper.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Atomic Resolution Cryogenic 4D-STEM Imaging via Robust Distortion Correction

Cryogenic four-dimensional scanning transmission electron microscopy (4D-STEM) imaging is a useful technique for studying quantum materials and their interfaces by simultaneously probing charge, lattice, spin, and chemistry on the atomic scale with the sample held at temperatures ranging from room to cryogenic. However, its applications are currently limited by the instabilities of cryo-stages and electronics. To overcome this challenge, we develop an algorithm to effectively correct the complex distortions present in atomic resolution cryogenic 4D-STEM data sets. This method uses nonrigid registration to identify localized distortions in a 4D-STEM and relate them to an undistorted experimental STEM image, followed by a series of affine transformations for distortion corrections. This method allows a minimum loss of information in both reciprocal and real spaces, enabling the reconstruction of sample information from 4D-STEM data sets. This method is computationally cheap, fast, and applicable for on-the-fly data analysis in future in situ cryogenic 4D-STEM experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Separable shape tensors for aerodynamic design

Airfoil shape design is a classical problem in engineering and manufacturing. In this work, we combine principled physics-based considerations for the shape design problem with modern computational techniques using a data-driven approach. Modern and traditional analyses of two-dimensional (2D) and three-dimensional (3D) aerodynamic shapes reveal a flow-based sensitivity to specific deformations that can be represented generally by affine transformations (rotation, scaling, shearing, and translation). We present a novel representation of shapes that decouples affine-style deformations over a submanifold and a product submanifold principally of the Grassmannian. As an analytic generative model, the separable representation, informed by a database of physically relevant airfoils, offers: (i) a rich set of novel 2D airfoil deformations not previously captured in the data, (ii) an improved low-dimensional parameter domain for inferential statistics informing design/manufacturing, and (iii) consistent 3D blade representation and perturbation over a sequence of nominal 2D shapes.

42 ENGINEERING↗

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

Revisiting the pseudo-supercritical path method: An improved formulation for the alchemical calculation of solid–liquid coexistence

Alchemical free energy calculations via molecular dynamics have been applied to obtain thermodynamic properties related to solid–liquid equilibrium conditions, such as melting points. In recent years, the pseudo-supercritical path (PSCP) method has proved to be an important approach to melting point prediction due to its flexibility and applicability. In the present work, we propose improvements to the PSCP alchemical cycle to make it more compact and efficient through a concerted evaluation of different potential energies. The multistate Bennett acceptance ratio (MBAR) estimator was applied at all stages of the new cycle to provide greater accuracy and uniformity, which is essential concerning uncertainty calculations. In particular, for the multistate expansion stage from solid to liquid, we employed the MBAR estimator with a reduced energy function that allows affine transformations of coordinates. Free energy and mean derivative profiles were calculated at different cycle stages for argon, triazole, propenal, and the ionic liquid 1-ethyl-3-methyl-imidazolium hexafluorophosphate. Comparisons showed a better performance of the proposed method than the original PSCP cycle for systems with higher complexity, especially the ionic liquid. Furthermore, a detailed study of the expansion stage revealed that remapping the centers of mass of the molecules or ions is preferable to remapping the coordinates of each atom, yielding better overlap between adjacent states and improving the accuracy of the methodology.

25 ENERGY STORAGE↗

3D reconstruction and neural rendering for adversarial machine learning

While evasion attacks on computer vision systems have been widely studied, creating attacks that remain effective under significant changes in viewpoint continues to be challenging. Traditional approaches often rely on affine transformations of images, but these approaches degrade at larger perspective shifts and often produce unrealistic or ineffective perturbations. Recent methods use differentiable renderers to improve viewpoint robustness, but they typically depend on manually constructed 3D models. We introduce a semi-automated pipeline that generates physically printable and perspective-invariant adversarial patches using only a small set of 2D images. Our method integrates 3D reconstruction, neural rendering, adversarial patch optimization, and an object detection victim model into a unified workflow. We use 2D Gaussian Splatting for high fidelity mesh reconstruction and FlexPara for surface parameterization that produces texture maps suitable for patch editing. Together, these components form a fully differentiable pipeline in PyTorch3D that links texture modification to model outputs, enabling efficient optimization of patches that remain effective across many viewpoints. The complete process, from image capture to patch printing and physical evaluation, can be completed within a few hours. We demonstrate the effectiveness of the resulting patches through attacks on the YOLOv8 object detection model and discuss remaining challenges and opportunities for improving robustness and scalability.

Singhvi, Vivaan [ORNL] (ORCID:0009000586288221)↗

radkit base v1.6

The radkit (base) software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices, cameras, as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations.

Salathe, Marco [Lawrence Berkeley National Laborat↗

G2Aero: A Python package for separable shape tensors

G2Aero is a Python package for the design and deformation of discrete planar curves and tubular surfaces using a geometric data-driven approach. G2Aero utilizes a topology of product manifolds: the Grassmannian, $\mathcal{G}$($\mathcal{n}$, 2) - the set of 2-dimensional subspaces in $\mathbb{R}$ $\mathcal{n}$ - and the symmetric positive-definite (SPD) manifold, $\mathcal{S}^{2}_{++}$ - the set of 2x2 SPD matrices. The package provides a novel framework for representing separable deformations to shapes, which consist of stretching, scaling, rotating, and translating - also known as affine deformations - and a set of complementary deformations - which we refer to as undulation-type deformations. We focus on airfoil and blade design applications to emphasize the utility of the methods in an environment where the separation of affine and undulation-type deformations is critical. Notable functionalities of the framework for blade design include: 1) generating novel 2D (airfoil) shapes informed by a database of physically relevant airfoils, 2) building 3D blades by interpolating sequences of 2D airfoil cross-sections, and 3) generating blades with consistent perturbations along the blade span. We discuss the framework and provide examples in the context of wind energy applications, specifically wind turbine blade design. Figure 1 shows the wire frame obtained by interpolating airfoils defining the IEA 15-MW wind turbine blade and applying affine transformations corresponding to twist, chordal scaling, and bending. This, and all other figures in the paper, can be reproduced following examples and referencing supporting documentation provided in the G2Aero package.

97 MATHEMATICS AND COMPUTING↗

Matching Curved Lattices to Anisotropic Tangent Planes

Radial quantization would be the ideal formalism for studying strongly-coupled near-conformal quantum field theories but it requires the ability to perform lattice calculations on static, curved manifolds, specifically a very long cylinder whose cross section is a sphere. Smoothly discretizing the surface of a sphere requires a graph with unequal edge lengths. The geometry of such graphs is well understood since 1961 using Regge Calculus. But, lattice quantum field theories are defined in terms of couplings which appear in the action rather than edge lengths and so the relationship between couplings and lengths must be determined dynamically. A simple example is computing the ratio of spatial to temporal lattice spacings in anisotropic lattice QCD. I will discuss our conjecture that computing anisotropic lattice spacing ratios on affine transformations of regular flat lattices is sufficient to determine coupling assignments on curved lattices.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Using Ultrasound Image Augmentation and Ensemble Predictions to Prevent Machine-Learning Model Overfitting

Deep learning predictive models have the potential to simplify and automate medical imaging diagnostics by lowering the skill threshold for image interpretation. However, this requires predictive models that are generalized to handle subject variability as seen clinically. Here, we highlight methods to improve test accuracy of an image classifier model for shrapnel identification using tissue phantom image sets. Using a previously developed image classifier neural network—termed ShrapML—blind test accuracy was less than 70% and was variable depending on the training/test data setup, as determined by a leave one subject out (LOSO) holdout methodology. Introduction of affine transformations for image augmentation or MixUp methodologies to generate additional training sets improved model performance and overall accuracy improved to 75%. Further improvements were made by aggregating predictions across five LOSO holdouts. This was done by bagging confidences or predictions from all LOSOs or the top-3 LOSO confidence models for each image prediction. Top-3 LOSO confidence bagging performed best, with test accuracy improved to greater than 85% accuracy for two different blind tissue phantoms. This was confirmed by gradient-weighted class activation mapping to highlight that the image classifier was tracking shrapnel in the image sets. Overall, data augmentation and ensemble prediction approaches were suitable for creating more generalized predictive models for ultrasound image analysis, a critical step for real-time diagnostic deployment.

60 APPLIED LIFE SCIENCES↗

Do Neural Networks Trained with Topological Features Learn Different Internal Representations?

There is a growing body of work that leverages features extracted via topological data analysis to train machine learning models. While this field, sometimes known as topological machine learning (TML), has seen some notable successes, an understanding of how the process of learning from topological features differs from the process of learning from raw data is still limited. In this work, we begin to address one component of this larger issue by asking whether a model trained with topological features learns internal representations of data that are fundamentally different than those learned by a model trained with the original raw data. To quantify ``different'', we exploit two popular metrics that can be used to measure the similarity of the hidden representations of data within neural networks, neural stitching and centered kernel alignment. From these we draw a range of conclusions about how training with topological features does and does not change the representations that a model learns. Perhaps unsurprisingly, we find that structurally, the hidden representations of models trained and evaluated on topological features differ substantially compared to those trained and evaluated on the corresponding raw data. On the other hand, our experiments show that in some cases, these representations can be reconciled (at least to the degree required to solve the corresponding task) using a simple affine transformation. We conjecture that this means that neural networks trained on raw data may extract some limited topological features in the process of making predictions.

McGuire, Sarah L.↗

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. In conclusion, solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.

60 APPLIED LIFE SCIENCES↗

Pulsed Light Synthesis of High Entropy Nanocatalysts with Enhanced Catalytic Activity and Prolonged Stability for Oxygen Evolution Reaction

The ability to synthesize compositionally complex nanostructures rapidly is a key to high-throughput functional materials discovery. In addition to being time-consuming, a majority of conventional materials synthesis processes closely follow thermodynamics equilibria, which limit the discovery of new classes of metastable phases such as high entropy oxides (HEO). Herein, a photonic flash synthesis of HEO nanoparticles at timescales of milliseconds is demonstrated. By leveraging the abrupt heating and cooling cycles induced by a high-power-density xenon pulsed light, mixed transition metal salt precursors undergo rapid chemical transformations. Hence, nanoparticles form within milliseconds with a strong affinity to bind to the carbon substrate. Oxygen evolution reaction (OER) activity measurements of the synthesized nanoparticles demonstrate two orders of magnitude prolonged stability at high current densities, without noticeable decay in performance, compared to commercial IrO 2 catalyst. This superior catalytic activity originates from the synergistic effect of different alloying elements mixed at a high entropic state. It is found that Cr addition influences surface activity the most by promoting higher oxidation states, favoring optimal interaction with OER intermediates. The proposed high-throughput method opens new pathways toward developing next-generation functional materials for various electronics, sensing, and environmental applications, in addition to renewable energy conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Trailblazing Kr/Xe Separation: The Birth of the First Kr-Selective Material

Efficient separation of Kr from Kr/Xe mixtures is pivotal in nuclear waste management and dark matter research. Thus far, scientists have encountered a formidable challenge: the absence of a material with the ability to selectively adsorb Kr over Xe at room temperature. This study presents a groundbreaking transformation of the renowned metal–organic framework (MOF) CuBTC, previously acknowledged for its Xe adsorption affinity, into an unparalleled Kr-selective adsorbent. This achievement stems from an innovative densification approach involving systematic compression of the MOF, where the crystal size, interparticle interaction, defects, and evacuation conditions are synergistically modulated. The resultant densified CuBTC phase exhibits exceptional mechanical resilience, radiation tolerance, and notably an unprecedented selectivity for Kr over Xe at room temperature. Simulation and experimental kinetic diffusion studies confirm reduced gas diffusion in the densified MOF, attributed to its small pore window and minimal interparticle voids. The lighter Kr element demonstrates facile surface passage and higher diffusivity within the material, while the heavier Xe encounters increased difficulty entering the material and lower diffusivity. This Kr-selective MOF not only represents a significant breakthrough in Kr separation but also demonstrates remarkable processability and scalability to kilogram levels. Furthermore, the findings presented herein underscore the transformative potential of engineered MOFs in addressing complex challenges, heralding a new era of Kr separation technologies.

36 MATERIALS SCIENCE↗

Abstraction of Hydride from Alkanes and Dihydrogen by the Perfluorotrityl Cation

Abstract Lewis acids play a central role in a large variety of chemical transformations. The reactivity of the strongest Lewis acids is typically studied in the context of affinity towards hard bases, such as fluoride or oxygenous species. Carbocations can be viewed as soft Lewis acids, possessing significant affinity for softer bases, such as hydride. This work presents the ambient‐temperature isolation of salts of the perfluorotrityl cation ((C 6 F 5 ) 3 C + or F 15 Tr + ) in combination with halogenated carborane anions. The F 15 Tr + cation exhibits remarkable hydride affinity, illustrated by the observation of hydride abstraction from dihydrogen, and of the rapid abstraction of hydride from −CH 2 −groups in alkanes. Theoretical studies support the favorability of hydride abstraction from dihydrogen, and indicate that the hydride abstraction from alkanes proceeds via a concerted hydride transfer process that is sensitive to steric effects.

Leong, Derek W. [Department of Chemistry Texas A&a↗