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DOE OSTI2024

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Predictive Phenomics Initiative Project Dataset Catalog Collection

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism↗

DOE OSTI2024

Modeling Clustered DNA Damage by Ionizing Radiation Using Multinomial Damage Probabilities and Energy Imparted Spectra

Simple and complex clustered DNA damage represent the critical initial damage caused by radiation. In this paper, a multinomial probability model of clustered damage is developed with probabilities dependent on the energy imparted to DNA and surrounding water molecules. The model consists of four probabilities: (A) direct damage of sugar-phosphate moieties leading to SSB, (B) OH− radical formation with subsequent SSB and BD formation, (C) direct damage to DNA bases, and (D) energy imparted to histone proteins and other molecules in a volume not leading to SSB or BD. These probabilities are augmented by introducing probabilities for the relative location of SSB using a ≤10 bp criteria for a double-strand break (DSB) and for the possible success of a radical attack that leads to SSB or BD. Model predictions for electrons, 4He, and 12C ions are compared to the experimental data and show good agreement. Thus, the developed model allows an accurate and rapid computational method to predict simple and complex clustered DNA damage as a function of radiation quality and to explore the resulting challenges to DNA repair.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Proton Acceleration in Low- β Magnetic Reconnection with Energetic Particle Feedback

Magnetic reconnection regions in space and astrophysics are known as active particle acceleration sites. There is ample evidence showing that energetic particles can take a substantial amount of converted energy during magnetic reconnection. However, there has been a lack of studies understanding the backreaction of energetic particles at magnetohydrodynamical scales in magnetic reconnection. To address this, we have developed a new computational method to explore the feedback by nonthermal energetic particles. This approach considers the backreaction from these energetic particles by incorporating their pressure into magnetohydrodynamics (MHD) equations. The pressure of the energetic particles is evaluated from their distribution evolved through Parker's transport equation, solved using stochastic differential equations (SDEs), so we coin the name MHD-SDE. Applying this method to low-β magnetic reconnection simulations, we find that reconnection is capable of accelerating a large fraction of energetic particles that contain a substantial amount of energy. When the feedback from these particles is included, their pressure suppresses the compression structures generated by magnetic reconnection, thereby mediating particle energization. Consequently, the feedback from energetic particles results in a steeper power-law energy spectrum. These findings suggest that feedback from nonthermal energetic particles plays a crucial role in magnetic reconnection and particle acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Buffer-IPyC separation process in TRISO fuel particles simulated with Bison code

During High Temperature Gas-cooled Reactor (HTGR) operation, tristructural isotropic (TRISO) coated-particle fuel undergoes irradiation-induced changes in morphology and thermomechanical properties. Experimental results from the Advanced Gas Reactor (AGR) Fuel Development and Qualification Program show, among other things, the mechanism of gap formation between the buffer and inner pyrolytic carbon (IPyC) layers, which could be explored further via computational simulations using the Bison code. Two simulation models were developed, the debonding restricted model, where no gap formation between buffer and IPyC layers is permitted, and the debonding enabled model, where the gap between those layers is created. The inputs of the simulated models are based on the irradiation conditions from the AGR-1 experiment. The research included simulations on spherical and aspherical fuel types. Under the specific temperatures and fluences of the AGR-1 irradiation experiment, and the Bison simulations, it was concluded that the most common scenario is a gap formation along the buffer-IPyC interface, while the least possible scenario is the situation where there is no gap formation at the buffer-IPyC junction. The computational results confirmed that the sphericity of the fuel influences the thickness of the gap that occurs at the buffer-IPyC junction, in a way that with increasing aspect ratio the gap thickness increases. The results obtained for spherical and aspherical fuel are nearly identical. Finally, performed simulations match conclusions observed from the AGR-1 experiment, which as such shows that the Bison code is a good computational method for simulating the TRISO fuel. Future simulations will include the validation of performed research and comparison of the results between Bison and PARFUME codes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Angular Correlation Date Measurements with the GeRMAC system

Advanced modeling and simulation efforts have improved at Idaho National Laboratory in recent years with a solid foundation of experimental results. Current computational methods represent significant modeling capabilities but are limited by the accuracy and availability of nuclear data. The creation of pre- and post-processing software tools to address these limitations is fundamental to the improvement of nuclear science modeling capacities. One aspect of predictive modeling tools deals with gamma-rays emitted from radionuclides, including fissile or fissionable material, fission products, or activation products, produced in reactor experiments or other neutron environments. The resulting radionuclides decay in unique ways, providing complications upon measurement as a result of random and cascade, or true, coincidence summing. These effects are not easily quantified during modeling efforts of gamma-ray source terms., The germanium rotational measurements for angular correlation (GeRMAC) system was built to quantify the relative angles for gamma rays emitted by radionuclides of interest to investigate true coincidence, or cascade, summing as well as the nuclear energy levels of decay schemes of interest. Proof of concept studies utilize a series of laboratory check sources to provide validity, and it will soon be used to perform the same measurements for fission products of interest. The resulting data can be used to implement into a Monte Carlo code, such as Geant4, to provide more precise gamma-ray source terms following irradiations of materials.

73 - NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

RidgeAlloy: A high pressure die casting alloy that captures the approaching wave of automotive body sheet scrap

Oak Ridge National Laboratory (ORNL) has recently launched an effort to economically expand the North American aluminum supply chain by designing and developing a new family of Al-Mg-Si-Fe-Mn structural die cast aluminum alloys that can be made from up to 100% mixed 5xxx and 6xxx series automotive post-consumer sheet scrap and do not require heat treatment. The goal is to develop an alloy capable of capturing the approaching scrap wave of aluminum sheet intensive vehicles (in the 2030’s) into integrated structural high pressure die castings, rather than down-cycling these high-grade sheet alloys into non-structural castings. ORNL discovered a significant gap in the commercial thermodynamic databases that were unable to predict the trends of a key primary intermetallic phase as a function of composition. Experiments were performed to correct this gap and to create a unique, corrected quaternary database for Al-Mg-Si-Fe. High throughput computational methods, including solidification simulations, were used to identify a composition volume capable of avoiding this embrittling primary intermetallic phase, even at higher Fe + Si contents. Laboratory scale castings validated the thermodynamic and solidification predictions and resulted in lab-cast alloys with little primary intermetallic, and which met or exceeded structural casting properties requirements for yield strength and ductility. An accelerated demonstration of an HPDC automotive part was conducted in collaboration with two U.S. small businesses. Ingots made from 100% recycled 5xxx and 6xxx series scrap (plus Fe) were used to die cast one variant of this new family of Al-Mg-Si-Fe-Mn alloys (with high Si + Fe content) into a mid-sized HPDC structural-type automotive component. The HPDC alloy demonstration part showed good properties (especially ductility) and good castability for a complex component.

Plotkowski, Alex [ORNL] (ORCID:0000000154718681)↗

DOE OSTI2026

Reconstruction of Six-Dimensional Phase Space

A phase space is a mathematical representation of all possible physical states of a system. Particle beams at Fermilab exist within a six-dimensional (6D) phase space defined by three positional components, (x, y, z) and three momentum components, (px, py, pz). To reconstruct this space implies taking measurement data from detectors and mapping out particle behavior using computational methods. The beam detectors, however, are only able to detect spatial distribution among the events of the beam, therefore being limited to positional data. Also, due to the vast number of events in a particle beam, it is extremely difficult to analyze and differentiate every single one’s behavior. However, with Machine Learning (ML), which can distinguish between patterns and map out particle behavior more efficiently. We first used the particle beam software, G4beamline, to simulate a 10,000-event muon beam, adjusting parameters such as initial momentum magnitude (p¬0) and virtual detector position. Using ten virtual detectors, we analyzed p0 values such that minimum 9,990 events were analyzed by every detector. We then input the data from these beam simulations to a C++ program, that randomly selects 100 events, and creates a 2D histogram based on spatial distribution, detector position, and event intensity. This process is repeated 100 times to create 100 histograms per p0 value. These images were then input to a modified ResNet18 Convolutional Neural Network (CNN) for training, and to predict p0 from some unseen set of histograms. The model was accurate when trained on momentum increments of 5 MeV/c and provided with denser training samples around highly variable test values. These results displayed machine learning being able to accurately predict p0 from being trained on different particle behaviors.

Shirlee, Jermain [Fermilab]↗

DOE OSTI2024

Posterior Covariance Matrix Approximations

Here, the Davis equation of state (EOS) is commonly used to model thermodynamic relationships for high explosive (HE) reactants. Typically, the parameters in the EOS are calibrated, with uncertainty, using a Bayesian framework and Markov Chain Monte Carlo (MCMC) methods. However, MCMC methods are computationally expensive, especially for complex models with many parameters. This paper provides a comparison between MCMC and less computationally expensive Variational methods (Variational Bayesian and Hessian Variational Bayesian) for computing the posterior distribution and approximating the posterior covariance matrix based on heterogeneous experimental data. All three methods recover similar posterior distributions and posterior covariance matrices. This study demonstrates that for this EOS parameter calibration application, the assumptions made in the two Variational methods significantly reduce the computational cost but do not substantially change the results compared to MCMC.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A comprehensive review of dwell time optimization methods in computer-controlled optical surfacing

Dwell time plays a vital role in determining the accuracy and convergence of the computer-controlled optical surfacing process. However, optimizing dwell time presents a challenge due to its ill-posed nature, resulting in non-unique solutions. To address this issue, several well-known methods have emerged, including the iterative, Bayesian, Fourier transform, and matrix-form methods. Despite their independent development, these methods share common objectives, such as minimizing residual errors, ensuring dwell time's positivity and smoothness, minimizing total processing time, and enabling flexible dwell positions. This paper aims to comprehensively review the existing dwell time optimization methods, explore their interrelationships, provide insights for their effective implementations, evaluate their performances, and ultimately propose a unified dwell time optimization methodology.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Should We Conserve Entropy or Energy when Computing CAPE with Mixed-Phase Precipitation Physics?

Abstract The rapidly increasing resolution of global atmospheric reanalysis and climate model datasets necessitates finding methods for computing convective available potential energy (CAPE) both efficiently and accurately. To this end, this article compares two common methods for computing CAPE which conserve either energy or entropy. Inaccuracies in these computations arise from both physical and numerical errors. For instance, computing CAPE with entropy conserved results in physical errors from nonequilibrium phase transitions but minimizes numerical errors because solutions are analytic at each height. In contrast, computing CAPE with energy conserved avoids these physical errors, but accumulates numerical errors that are grid-resolution-dependent because the numerical integration of a differential equation is required. Analysis of CAPE computed with large databases of soundings from the tropical Amazon and midlatitude storm environments shows that physical errors from the entropy method are typically 1%–3% as large as CAPE, which is comparable to the numerical errors from conserving energy with grid spacing of 25 and 250 m using explicit first-order and second-order integration schemes, respectively. Errors in entropy-based CAPE calculations are also insensitive to vertical grid spacing, in contrast to energy-based calculations whose error strongly scales with the grid spacing. It is shown that entropy-based methods are advantageous when intercomparing datasets with differing vertical resolution because they produce accurate and reasonably fast results that are insensitive to grid resolution, whereas a second-order energy-based method is advantageous when analyzing data with a consistent vertical resolution because of its superior computational efficiency. Significance Statement Convective available potential energy (CAPE) is a measure of instability in the atmosphere that helps forecasters and researchers understand when and where thunderstorms will form. The purpose of this article is to identify the most efficient and accurate methods for computing CAPE. Two methods are considered here, one that relates to the entropy (a measure of thermodynamic disorder) of an air parcel and one that relates to the energy of an air parcel. Results indicate that the entropy method is most accurate and insensitive to the resolution of the data used for the calculation (which can vary considerably), whereas the energy method uses the least computation time.

Peters, John M.↗

DOE OSTI2025

Enhancing ACPF Analysis: Integrating Newton-Raphson Method with Gradient Descent and Computational Graphs

This paper presents a new method for enhancing Alternating Current Power Flow (ACPF) analysis. The method integrates the Newton-Raphson (NR) method with Enhanced-Gradient Descent (GD) and computational graphs. The integration of renewable energy sources in power systems introduces variability and unpredictability, and this method addresses these challenges. It leverages the robustness of NR for accurate approximations and the flexibility of GD for handling variable conditions, all without requiring Jacobian matrix inversion. Furthermore, computational graphs provide a structured and visual framework that simplifies and systematizes the application of these methods. The goal of this fusion is to overcome the limitations of traditional ACPF methods and improve the resilience, adaptability, and efficiency of modern power grid analyses. We validate the effectiveness of our advanced algorithm through comprehensive testing on established IEEE benchmark systems. Furthermore, our findings demonstrate that our approach not only speeds up the convergence process but also ensures consistent performance across diverse system states, representing a significant advancement in power flow computation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Probabilistic Resilience-Oriented Assessment Approach for Transmission Networks Under Wildfires

The rising threat of wildfires poses significant challenges to power transmission networks, particularly in areas prone to such disasters. Traditional approaches for wildfire risk assessment neglect some potential wildfire scenarios. Here, this paper introduces a probabilistic resilience-oriented assessment approach for power transmission networks to address this gap. Initially, a probabilistic wildfire model is developed to capture uncertainties in ignition, intensity, and fire spread. Next, a spatiotemporal fragility model is constructed to assess the impact of wildfires on transmission corridors, incorporating Thermal Aging (TA) and Dynamic Thermal Rate (DTR) change. Finally, a comprehensive resilience metric is defined to evaluate system performance, leveraging the fragility model to determine component and system-level resilience. The approach employs a combinatorial enumeration method to generate potential wildfire scenarios, enhanced by an impact-increment-based state enumeration (IISE) method for computational efficiency. The proposed method provides critical insights for identifying system vulnerabilities and developing robust strategies to protect transmission networks from wildfires. The efficacy of this approach is validated through extensive scenarios of the RTS-GMLC system across Southern California, Nevada and Arizona.

Vahedi, Soroush [Univ. of Connecticut, Storrs, CT ↗

DOE OSTI2026

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Leveraging Natural Language Processing and Generative Models in Molecular Chemistry: Property Prediction and Novel Compound Generation

The accurate prediction of molecular properties is important for the rational design and the advancement of green chemistry and sustainable materials research. However, the predictive power of traditional computational chemistry methods is limited due to computational restrictions. Here, in this study, we examine an alternative approach to the accurate prediction of properties of organic compounds: natural language processing (NLP)-based molecular embedding. Using viscosity, partition coefficient (log P), and enthalpy of vaporization as test properties through a survey of comprehensive datasets comprising 5695 data points for viscosity, 25 870 data points for log P, and 2296 data points for enthalpy of vaporization. These are important properties for the design of greener, safer, and sustainable chemical processes. Models were trained using NLP methods such as Mol2vec and fine-tuned ChemBERTa, and results were compared with traditional input featurization techniques such as Morgan fingerprints and quantum chemistry derived sigma profiles and DFT features. Among the various machine learning models, Mol2vec demonstrated superior predictive capabilities, achieving the highest correlation coefficient (R 2 = 0.945) and lowest RMSE (0.106 mPa s) for viscosity, as well as high accuracy for log P and enthalpy of vaporization predictions. These findings establish the Mol2vec featurization technique, graph-convolutional neural networks (GCNN), and fine-tuned ChemBERTa model as powerful tools for predictive modeling of organic compounds properties, offering a significant improvement over previously used featurization techniques and opening up strategies for very-high-throughput computational screening. Finally, we integrated ML models with hybrid language-model-based generative adversarial networks (LM-GAN) to generate novel molecular sequences with desirable properties for different research applications. The ability to computationally design solvents with lower viscosity, lower log P, and lower enthalpy of vaporization offers a data-driven route to accelerating the discovery of sustainable alternatives to traditionally toxic solvents.

ChemBERTa↗

DOE OSTI2024

Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆

Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.

additive Schwarz solvers↗

DOE OSTI2025

Classical eikonal from Magnus expansion

In a classical scattering problem, the classical eikonal is defined as the generator of the canonical transformation that maps in-states to out-states. It can be regarded as the classical limit of the log of the quantum S-matrix. In a classical analog of the Born approximation in quantum mechanics, the classical eikonal admits an expansion in oriented tree graphs, where oriented edges denote retarded/advanced worldline propagators. The Magnus expansion, which takes the log of a time-ordered exponential integral, offers an efficient method to compute the coefficients of the tree graphs to all orders. We exploit a Hopf algebra structure behind the Magnus expansion to develop a fast algorithm which can compute the tree coefficients up to the 12th order (over half a million trees) in less than an hour. In a relativistic setting, our methods can be applied to the post-Minkowskian (PM) expansion for gravitational binaries in the worldline formalism. We demonstrate the methods by computing the 3PM eikonal and find agreement with previous results based on amplitude methods. Importantly, the Magnus expansion yields a finite eikonal, while the naïve eikonal based on the time-symmetric propagator is infrared-divergent from 3PM on.

Black Holes↗