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DOE OSTI2025

Water Mass Transformation Budgets in Finite‐Volume Generalized Vertical Coordinate Ocean Models

Water Mass Transformation (WMT) theory provides conceptual tools that in principle enable innovative analyses of numerical ocean models; in practice, however, these methods can be challenging to implement and interpret, and therefore remain under-utilized. Our aim is to demonstrate the feasibility of diagnosing all terms in the water mass budget and to exemplify their usefulness for scientific inquiry and model development by quantitatively relating water mass changes, overturning circulations, boundary fluxes, and interior mixing. We begin with a pedagogical derivation of key results of classical WMT theory. We then describe best practices for diagnosing each of the water mass budget terms from the output of Finite-Volume Generalized Vertical Coordinate (FV-GVC) ocean models, including the identification of a non-negligible remainder term as the spurious numerical mixing due to advection scheme discretization errors. We illustrate key aspects of the methodology through the analysis of a polygonal region of the Greater Baltic Sea in a regional demonstration simulation using the Modular Ocean Model v6 (MOM6). We verify the convergence of our WMT diagnostics by brute-force, comparing time-averaged (“offline”) diagnostics on various vertical grids to timestep-averaged (“online”) diagnostics on the native model grid. Finally, we briefly describe a stack of xarray-enabled Python packages for evaluating WMT budgets in FV-GVC models (culminating in the new xwmb package), which is intended to be model-agnostic and available for community use and development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Data-driven organic solubility prediction at the limit of aleatoric uncertainty

Abstract Small molecule solubility is a critically important property which affects the efficiency, environmental impact, and phase behavior of synthetic processes. Experimental determination of solubility is a time- and resource-intensive process and existing methods for in silico estimation of solubility are limited by their generality, speed, and accuracy. This work presents two models derived from the FASTPROP and CHEMPROP architectures and trained on BigSolDB which are capable of predicting solubility at arbitrary temperatures for a wide range of small molecules in organic solvent. Both extrapolate to unseen solutes 2–3 times more accurately than the current state-of-the-art model and we demonstrate that they are approaching the aleatoric limit (0.5–1$$\log S$$ log S ) of available test data, suggesting that further improvements in prediction accuracy require more accurate datasets. The FASTPROP-derived model (called FASTSOLV) and the CHEMPROP-based model are open source, freely accessible via a Python package and web interface, highly reproducible, and up to 2 orders of magnitude faster than current alternatives.

Science & Technology - Other Topics↗

DOE OSTI2024

Physics and chemistry from parsimonious representations: image analysis via invariant variational autoencoders

Electron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine learning methods for discovery of physical and chemical phenomena from the data, such as manifestations of symmetry breaking phenomena in electron and scanning tunneling microscopy images, or variability of the nanoparticles. Variational autoencoders (VAEs) are emerging as a powerful paradigm for the unsupervised data analysis, allowing to disentangle the factors of variability and discover optimal parsimonious representation. Here, we summarize recent developments in VAEs, covering the basic principles and intuition behind the VAEs. The invariant VAEs are introduced as an approach to accommodate scale and translation invariances present in imaging data and separate known factors of variations from the ones to be discovered. We further describe the opportunities enabled by the control over VAE architecture, including conditional, semi-supervised, and joint VAEs. Several case studies of VAE applications for toy models and experimental datasets in Scanning Transmission Electron Microscopy are discussed, emphasizing the deep connection between VAE and basic physical principles. Python codes and datasets discussed in this article are available at https://github.com/saimani5/VAE-tutorials and can be used by researchers as an application guide when applying these to their own datasets.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry

Graph deep learning models, which incorporate a natural inductive bias for atomic structures, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, MatGL is designed to be an extensible “batteries-included” library for developing advanced model architectures for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also provides several pre-trained foundation potentials (FPs) with coverage of the entire periodic table, and property prediction models for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL integrates with PyTorch Lightning to enable efficient model training.

chemistry↗

DOE OSTI2024

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗

DOE OSTI2025

A framework to evaluate machine learning crystal stability predictions

The rapid adoption of machine learning in various scientific domains calls for the development of best practices and community agreed-upon benchmarking tasks and metrics. We present Matbench Discovery as an example evaluation framework for machine learning energy models, here applied as pre-filters to first-principles computed data in a high-throughput search for stable inorganic crystals. We address the disconnect between (1) thermodynamic stability and formation energy and (2) retrospective and prospective benchmarking for materials discovery. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with adaptive user-defined weighting of various performance metrics allowing researchers to prioritize the metrics they value most. To answer the question of which machine learning methodology performs best at materials discovery, our initial release includes random forests, graph neural networks, one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials. We highlight a misalignment between commonly used regression metrics and more task-relevant classification metrics for materials discovery. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV per atom above the convex hull. The benchmark results demonstrate that universal interatomic potentials have advanced sufficiently to effectively and cheaply pre-screen thermodynamic stable hypothetical materials in future expansions of high-throughput materials databases.

Riebesell, Janosh↗

DOE OSTI2026

An end-to-end workflow for executing a classically bootstrapped variational quantum algorithm on an academic quantum computer

Academic quantum computing platforms often face unique challenges in executing quantum workloads due to fragmented software environments and limited engineering support. Unlike commercial ecosystems, academic devices typically evolve without full-stack integration in mind, making it difficult to run complex applications—such as variational quantum algorithms (VQA)—reliably and efficiently. Issues such as incompatible software layers and lack of automated job management significantly increase the overhead of theory-experiment collaboration. To address these challenges, we develop a modular, end-to-end workflow that decouples application-layer code from low-level hardware control, automates circuit submission and result collection, and supports fine-grained circuit-level job scheduling and recovery. The architecture employs a dual-end application programming interface (API) design, enabling robust operation across unstable or resource-constrained hardware backends. For practical use, the framework is lightweight and user-friendly, allowing rapid prototyping of full-stack workflows using basic Python tools. We validate this workflow on a high-fidelity trapped-ion quantum computer by demonstrating a variational quantum eigensolver (VQE) experiment with a classically bootstrapped ansatz initialization technique. The system successfully executed over 60,000 circuits across multiple molecular test cases with minimal human intervention, highlighting the framework’s effectiveness in enabling reproducible, resilient quantum experimentation in academic settings.

Clifford↗

DOE OSTI2025

TOFHunter—unlocking rapid untargeted screening of inductively coupled plasma–time-of-flight–mass spectrometry data

This study provides an overview of a newly developed open source program written in Python, TOFHunter, which permits the rapid and untargeted screening of inductively coupled plasma (ICP)-time-of-flight (TOF)-mass spectrometry (MS) datasets. ICP-TOF-MS is an analytical tool capable of providing quasi simultaneous detection of all nuclides from Li to Pu. This capability has triggered an increase in studies investigating single-particle analysis in which the TOF-MS provides correlated elemental/isotopic signatures on a particle basis in time. Similarly, laser ablation mapping has seen rapid growth owing to ICP-TOF-MS's capacity to handle fast washout times (<10 ms) while providing a broad nuclide coverage. The caveat to this broad mass coverage and high time resolution comes in the form of large, overwhelming datasets. With datasets typically on the scale of gigabytes, it is easy for a user to only focus on very targeted analytes; however, this focus diminishes the opportunity offered by the TOF-MS detector. TOFHunter applies chemometric methods, principal component analysis (PCA), and interesting features finder (IFF) on ICP-TOF-MS data, allowing for investigation of correlations, major and minor variance sources, and sample screening. The unique spectra identified by the (IFF) are used to generate a list of mass peaks, which are then matched with both nuclides and potential interferences before being exported for the user to investigate. Several case studies are discussed herein, demonstrating TOFHunter's ability to screen aqueous injections, single-particle/single-cell analysis, and probe laser ablation mapping files for unique regions of interest.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Autonomous organic synthesis for redox flow batteries via flexible batch Bayesian optimization

Traditional trial-and-error methods for materials discovery are inefficient to meet the urgent demands posed by the rapid progression of climate change. This urgency has driven the increasing interest in integrating robotics and machine learning into materials research to accelerate experimental learning. However, idealized decision-making frameworks to achieve maximum sampling efficiency are not always compatible with high-throughput experimental workflows inside a laboratory. For multi-step chemical processes, differences in hardware capacities can complicate the digital framework by introducing constraints on the maximum number of samples in each step of the experiment, hence causing varying batch sizes in variable selection within the same batch. Therefore, designing flexible sampling algorithms is necessary to accommodate the multi-step synthesis with practical constraints unique to each high-throughput workflow. In this work, we designed and employed three strategies on a high-throughput robotic platform to optimize the sulfonation reaction of redox-active molecules used in flow batteries. Our strategies adapt to the multi-step experimental workflow, where their formulation and heating steps are separate, causing varying batch size requirements. By strategically sampling using clustering and mixed-variable batch Bayesian optimization, we were able to iteratively identify optimal conditions that maximize the yields. Our work presents a flexible approach that allows tailoring the machine learning decision-making to suit the practical constraints in individual high-throughput experimental platforms, followed by performing resource-efficient yield optimization using available open-source Python libraries.

Tamura, Clara [Univ. of Washington, Seattle, WA (U↗

DOE OSTI2025

Active Learning of Microgrid Frequency Dynamics Using Neural Ordinary Differential Equations

Accurate frequency modelling of inverter‐based resource (IBR)‐dominated power systems is crucial for ensuring stable, reliable and resilient operations, particularly given their inherent low‐inertia characteristics and fast dynamics that traditional swing equation‐based models inadequately capture. This paper explores neural ordinary differential equations (Neural ODEs) as a computationally efficient, data‐driven framework for modelling power system frequency dynamics, specifically within microgrids integrating high penetrations of distributed energy resources (DERs). The developed neural ODEs framework incorporates a neural network architecture designed to capture input dynamics. By actively perturbing the system with a known signal, the Python‐based neural ODEs framework was trained using measured system states and inputs, without the need for detailed system information. The framework, tested on a model of the Cordova, AK, microgrid, achieved a goodness of fit ranging from 60% to 99% across different state variables and maintained a mean square error in the 10 -6 p.u. range under square and step excitation signals. The proposed approach demonstrated robustness to measurement noise and initial condition variations while maintaining low computational complexity suitable for real‐time power system control applications. Furthermore, transfer learning enabled the neural ODEs model to adapt to the following changes in system topology or generator dispatch, highlighting its effectiveness for dynamic microgrids with frequently evolving configurations and diverse DERs.

Aryal, Tara [South Dakota State Univ., Brookings, ↗

DOE OSTI2024

FORSE+: Simulating non-Gaussian CMB foregrounds at 3 arcmin in a stochastic way based on a generative adversarial network

We present FORSE+, a Python package that produces non-Gaussian diffuse Galactic thermal dust emission maps at arcminute angular scales and that has the capacity to generate random realizations of small scales. This represents an extension of the FORSE (Foreground Scale Extender) package, which was recently proposed to simulate non-Gaussian small scales of thermal dust emission using generative adversarial networks (GANs). With the input of the large-scale polarization maps from observations, FORSE+ has been trained to produce realistic polarized small scales at 3′ following the statistical properties, mainly the non-Gaussianity, of observed intensity small scales, which are evaluated through Minkowski functionals. Furthermore, by adding different realizations of random components to the large-scale foregrounds, we show that FORSE+ is able to generate small scales in a stochastic way. In both cases, the output small scales have a similar level of non-Gaussianity compared with real observations and correct amplitude scaling as a power law. These realistic new maps will be useful, in the future, to understand the impact of non-Gaussian foregrounds on the measurements of the cosmic microwave background (CMB) signal, particularly on the lensing reconstruction, de-lensing, and the detection of cosmological gravitational waves in CMB polarizationB-modes.

Astronomy & Astrophysics↗

DOE OSTI2024

Geant4 Monte-Carlo (GEMC) A database-driven simulation program

GEMC[1] is an application that harnesses the power of databases to execute Geant4 Monte-Carlo simulations. The databases (MYSQL, CSQL, TEXT) define the geometry, materials, digitization algorithms, readout electronics and output formats. Implemented in C++, GEMC also boasts a user-friendly Python API that facilitates detector construction and database population. GEMC can handle real-life scenarios such as geometry variations and the run number-dependent calibration constants and digitization parameters. This abstract provides an overview of GEMC, accompanied by examples that showcase its versatility. We delve into the practical application of GEMC within the the CLAS12 experimental program at Jefferson Lab.

Ungaro, Maurizio↗

DOE OSTI2024

Geospatial Capabilities to Couple Hazard and Social Vulnerability Data in Water Distribution Criticality Analysis

A resilience analysis of a water distribution system is greatly enhanced by the integration of up-to-date geospatial data describing the water system, hazards, and surrounding community. The Water Network Tool for Resilience (WNTR), an open-source Python package designed to simulate and analyze the resilience of water distribution systems, was recently updated to incorporate geographic information system (GIS) data into the resilience analysis. This paper describes the GIS capabilities and includes a case study using the drinking water distribution system model for a large city in Pennsylvania. The case study focuses on potential pipe damage from landslides and on pipes that are particularly difficult to repair. The analysis couples data on hazards, social vulnerability, and the location of emergency services to identify and prioritize high-impact critical infrastructure for mitigation. Results demonstrate that pipes can be prioritized for mitigation based on water shortage and vulnerable populations that are affected. In conclusion, the methods can be adopted for general use and are available as part of the WNTR software.

GIS, landslide↗

DOE OSTI2025

Computational toolkit for predicting thickness of 2D materials using machine learning and autogenerated dataset by large language model

The thickness of 2D materials not only plays a crucial role in determining the performance of nanoelectronic and optoelectronic devices but also introduces complexities in predicting volume-dependent properties, such as energy storage capacity, due to the intrinsic vacuum within these materials. Although a plethora of experimental techniques, including but not limited to optical contrast, Raman spectroscopy, nonlinear optical spectroscopy, near-field optical imaging, and hyperspectral imaging, facilitate the measurement of 2D material thickness, comprehensive data for many materials remain elusive. Over the past decade, the exponential proliferation of 2D materials and their heterostructures has outstripped the capabilities of conventional experimental and computational approaches. In this evolving landscape, machine learning (ML) has emerged as an indispensable tool, offering a scalable approach to augment these traditional methodologies. Addressing the critical gap, we introduce THICK2D—Thickness Hierarchy Inference and Calculation Kit for 2D Materials. This Python-based computational framework harnesses an autogenerated thickness database, developed using large language models, and advanced ML algorithms to facilitate the rapid and scalable estimation of material thickness, relying solely on crystallographic data. To demonstrate the utility and robustness of THICK2D, we successfully used the toolkit to predict the thickness of more than 8000 2D-based materials, sourced from two extensive 2D materials databases. THICK2D is disseminated as an open-source utility, accessible on GitHub at https://github.com/gmp007/THICK2D, and archived on Zenodo at https://10.5281/zenodo.11216648.

Ekuma, Chinedu E. (ORCID:0000000258527556)↗

DOE OSTI2025

Tree tensor network hierarchical equations of motion based on time-dependent variational principle for efficient open quantum dynamics in structured thermal environments

In this work, we introduce an efficient method, TTN-HEOM, for exactly calculating the open quantum dynamics for driven quantum systems interacting with highly structured bosonic baths by combining the tree tensor network (TTN) decomposition scheme with the bexcitonic generalization of the numerically exact hierarchical equations of motion (HEOM). The method yields a series of quantum master equations for all core tensors in the TTN that efficiently and accurately capture the open quantum dynamics for non-Markovian environments to all orders in the system–bath interaction. These master equations are constructed based on the time-dependent Dirac–Frenkel variational principle, which isolates the optimal dynamics for the core tensors given the TTN ansatz. The dynamics converges to the HEOM when increasing the rank of the core tensors, a limit in which the TTN ansatz becomes exact. We introduce TENSO, tensor equations for non-Markovian structured open systems, as a general-purpose Python code to propagate the TTN-HEOM dynamics. We implement three general propagators for the coupled master equations: two fixed-rank methods that require a constant memory footprint during the dynamics and one adaptive-rank method with a variable memory footprint controlled by the target level of computational error. We exemplify the utility of these methods by simulating a two-level system coupled to a structured bath containing one Drude–Lorentz component and eight Brownian oscillators, which is beyond what can presently be computed using the standard HEOM. Our results show that the TTN-HEOM is capable of simulating both dephasing and relaxation dynamics of driven quantum systems interacting with structured baths, even those of chemical complexity, with an affordable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Orbit-averaging and deposition accuracy for runaway electron beams in hybrid kinetic-MHD simulations of the runaway plateau

We develop a new procedure that combines the kinetic orbit runaway electron code (KORC) and the NIMROD extended-magnetohydrodynamic code to simulate runaway electrons (REs) in the post-disruption plateau. KORC integrates guiding-center orbits, with a barycentric-based binary search strategy providing initial guesses for the Newton–Raphson logical-to-physical coordinate inversion, ensuring reliable particle-to-mesh mapping in NIMROD, whose fields remain static for the present study. Samples are drawn in accord with experimental parallel current profiles of RE beams during the plateau phase. Deposition in NIMROD is verified through comparison with a Python-based finite-element code that ensures periodicity in the poloidal direction and continuity at the magnetic axis. Accurate representation of near-axis fields requires finer mesh resolution to prevent under- and overshoots in current density from orbit inaccuracies. Yet, at a fixed particle count, increasing mesh resolution amplifies statistical noise in the deposited fields. An orbit-averaging method accumulates partial current deposits over multiple kinetic steps and reduces the statistical noise with little added computational cost. By coupling kinetic routines from KORC directly into the NIMROD codebase, these developments lay essential groundwork for future self-consistent KORC–NIMROD coupling.

Algorithms and data structure↗