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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2025

Cosmological Hydrodynamics at Exascale: A Trillion-Particle Leap in Capability

Resolving the most fundamental questions in cosmology requires simulations that match the scale, fidelity, and physical complexity demanded by next-generation sky surveys. To achieve the realism needed for this critical scientific partnership, detailed gas dynamics must be treated self-consistently with gravity for end-to-end modeling of structure formation. Exascale computing enables simulations that span survey-scale volumes while incorporating key astrophysical processes that shape complex cosmic structures. We present results from CRK-HACC, a cosmological hydrodynamics code built for extreme scalability. Using separation-of-scale techniques, GPU-resident tree solvers, in situ analysis pipelines, and multi-tiered I/O, CRK-HACCexecuted Frontier-E: a four trillion particle full-sky simulation, over an order of magnitude larger than previous efforts. The run achieved 513.1 PFLOPs peak performance, processing 46.6 billion particles per second and writing more than 100 PB of data in just over one week of runtime. Frontier-E marks a significant advance in predictive modeling for next-generation cosmological science.

Frontiere, Nicholas [Argonne National Laboratory (↗
DOE OSTI2026

Neural operator transformers capture bifurcating drift-wave turbulence in fusion plasma simulations

Self-consistent modeling of turbulence-driven transport is critical for optimizing confinement in magnetically confined fusion plasmas, such as tokamaks and stellarators. In particular, capturing the long-term co-evolution of turbulence, flow, and background plasma profiles remains computationally challenging. Direct numerical simulation of these multiscale, highly nonlinear processes is often demanding and impractical for real-time control or design optimization. To address this bottleneck, we investigate transformer-based neural operator partial differential equation surrogates for emulating the dynamics of drift-wave turbulence bifurcation mediated by zonal flows, using the modified Hasegawa–Wakatani (MHW) model as a prototypical system. We find that the finetuned neural operator model has excellent performance in capturing the multi-spatiotemporal-scales of MHW turbulence bifurcation and is robust to testing on rare and out-of-distribution dynamics. Specifically, we demonstrate that a single unified model accurately predicts both quasi-steady-state turbulence and a wide range of dynamical transition processes, such as nonlinear saturation, spontaneous suppression of turbulence, and the emergence of macroscopic zonal flows, over time horizons vastly exceeding the local turbulence correlation time. This computationally efficient approach establishes a strong foundation for fast, AI-based modeling of complex, multiscale phenomena in magnetized fusion plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Automatic building energy model development and debugging using large language models agentic workflow

Building energy modeling (BEM) is a complex process that demands significant time and expertise, limiting its broader application in building design and operations. While Large Language Models (LLMs) agentic workflow have facilitated complex engineering processes, their application in BEM has not been specifically explored. This paper investigates the feasibility of automating BEM using LLM agentic workflow. Here, we developed a generic LLM-planning-based workflow that takes a building description as input and generates an error-free EnergyPlus building energy model. Our robust workflow includes four core agents: 1) Building Description Pre-Processing, 2) IDF Object Information Extraction, 3) Single IDF Object Generator Suite, and 4) IDF Debugging Agent. These agents divide the complex tasks into manageable sub-steps, enabling LLMs to generate accurate and reliable results at each stage. The case study demonstrates the successful translation of a building description into an error-free EnergyPlus model for the iUnit modular building at the National Renewable Energy Laboratory. The effectiveness of our workflow surpasses: 1) naive prompt engineering, 2) other LLM-based workflows, and 3) manual modeling, in terms of accuracy, reliability, and time efficiency. The paper concludes with a discussion on the interplay between foundational models and LLM agent planning design, advocating for the use of fine-tuned, specialized models to advance this field.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Accurate noncovalent interactions in atomistic systems via quantum Drude oscillators

Accurately modeling polarization and van der Waals (vdW) interactions in atomistic systems typically requires high-level quantum-mechanical methods that are computationally expensive, hence limited in applicability. To address this challenge, efficient yet physically grounded models are needed—ones that not only enable accurate predictions but also provide insight into how noncovalent interactions scale in complex molecular and material systems. This review highlights the quantum Drude oscillator (QDO) model, a physically motivated and computationally efficient framework that captures the essential features of electronic response, including polarization and dispersion forces, across a wide range of chemical and material systems. We discuss how the QDO model quantitatively reproduces the polarization response of many-electron atoms and how key components of noncovalent interactions—exchange-repulsion, polarization, and dispersion—emerge naturally in QDO dimers. Furthermore, the model provides predictive scaling laws that elucidate trends in polarizability and dispersion across the periodic table and in molecular assemblies. By uniting interpretability, accuracy, and efficiency, the QDO model offers a versatile approach for modeling noncovalent interactions in systems ranging from isolated molecules to complex condensed phases and nanostructured materials.

Khabibrakhmanov, Almaz [Univ. of Luxembourg, Luxem↗
DOE OSTI2024

Learning nonlinear operators in latent spaces for real-time predictions of complex dynamics in physical systems

Abstract Predicting complex dynamics in physical applications governed by partial differential equations in real-time is nearly impossible with traditional numerical simulations due to high computational cost. Neural operators offer a solution by approximating mappings between infinite-dimensional Banach spaces, yet their performance degrades with system size and complexity. We propose an approach for learning neural operators in latent spaces, facilitating real-time predictions for highly nonlinear and multiscale systems on high-dimensional domains. Our method utilizes the deep operator network architecture on a low-dimensional latent space to efficiently approximate underlying operators. Demonstrations on material fracture, fluid flow prediction, and climate modeling highlight superior prediction accuracy and computational efficiency compared to existing methods. Notably, our approach enables approximating large-scale atmospheric flows with millions of degrees, enhancing weather and climate forecasts. Here we show that the proposed approach enables real-time predictions that can facilitate decision-making for a wide range of applications in science and engineering.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach

Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Defect Complexes in CrSBr Revealed Through Electron Microscopy and Deep Learning

Atomic defects underpin the properties of van der Waals materials, and their understanding is essential for advancing quantum and energy technologies. Scanning transmission electron microscopy is a powerful tool for defect identification in atomically thin materials, and extending it to multilayer and beam-sensitive materials would accelerate their exploration. Here, we establish a comprehensive defect library in a bilayer of the magnetic quasi-1D semiconductor CrSBr by combining atomic-resolution imaging, deep learning, and calculations. We apply a custom-developed machine learning work flow to detect, classify, and average point vacancy defects. This classification enables us to uncover several distinct Cr interstitial defect complexes, combined Cr and Br vacancy defect complexes, and lines of vacancy defects that extend over many unit cells. We show that their occurrence is in agreement with our computed structures and binding energy densities, reflecting the intriguing layer interlocked crystal structure of CrSBr. Our ab initio calculations show that the interstitial defect complexes give rise to highly localized electronic states. These states are of particular interest due to the reduced electronic dimensionality and magnetic properties of CrSBr and are, furthermore, predicted to be optically active. Our results broaden the scope of defect studies in challenging materials and reveal new defect types in bilayer CrSBr that can be extrapolated to the bulk and to over 20 materials belonging to the same FeOCl structural family.

deep learning↗
DOE OSTI2025

Towards the Stable Chelation of Radioantimony(V) for Targeted Auger Theranostics

Antimony-119 ( 119 Sb) is one of the most attractive Auger-electron emitters identified to date, but it remains practically unexplored for targeted radiotherapy because no chelators have been identified to stably bind this metalloid in vivo. In a departure from current studies focused on chelator development for Sb(III), we explore the chelation chemistry of Sb(V) using the tris-catecholate ligand TREN-CAM. Through a combination of radiolabeling, spectroscopic, solid-state, and computational studies, the radiochemistry and structural chemistry of TREN-CAM with 1XX/nat Sb(V) were established. The resulting [ 1XX Sb]Sb–TREN-CAM complex remained intact for several days in human serum, signifying high stability under biological conditions. Finally, the first in vivo single photon emission computed tomography and positron emission tomography imaging studies were carried out using 117 Sb, the diagnostic analogue of 119 Sb. These studies revealed marked differences in the uptake and distribution of activity in mice administered unchelated [ 117 Sb]Sb(OH) 6 – versus [ 117 Sb]Sb–TREN-CAM, suggesting that 117 Sb is largely retained by TREN-CAM over the time course of the study. Collectively, these findings demonstrate the most physiologically stable complex of no-carrier-added 1XX Sb yet reported, offering new promise for the clinical implementation of radioantimony in nuclear medicine. In conclusion, our results also establish the feasibility of 117 Sb as an elementally matched partner to 119 Sb for theranostic applications.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Full-wave modeling of RF waves in fusion plasmas with finite element method: Progress in past decades and its future role

This paper reviews the progress in computing radio frequency (RF) wave fields in fusion plasmas, specifically focusing on simulations utilizing the finite element method (FEM) over the past few decades. Computing RF wave fields in fusion plasmas presents unique challenges due to large simulation domains, complex antenna structures, non-local dielectric properties, and wide ranges of spatial scales. It highlights key developments and outlines future directions, primarily addressing waves in the ion cyclotron (IC) to lower hybrid (LH) frequency range. We begin with briefly revisiting earlier developments before the widespread availability of modern computer-aided engineering (CAE) software based on FEM. This historical perspective illuminates early progress and the physics difficulties that motivated ongoing work within the community. Modern wave simulations for RF antennas based on FEM are characterized by the use of detailed 3D antenna model geometry generated from engineering CAD software and localized wave dielectric model. Significant advancements have also been made in improving physics models to include phenomena such as RF sheath rectification and wave scattering. FEM-based RF simulations have also been applied to compute wave propagation in the core region, where the inclusion of non-local dielectric response is crucial. This is a challenging goal, and several promising approaches have been proposed in this area. Additionally, RF simulation development initiatives based on open-source libraries have gained popularity, demonstrating scalability and flexibility in extending physics models. This paper will discuss the advantages and disadvantages of using such a publicly available FEM library.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

2025 Workshop on Envisioning Frontiers in AI and Computing for Biological Research: Position Papers

This workshop aims to identify key research directions for transforming biology using artificial intelligence (AI), machine learning (ML) and computational methods to facilitate the discovery of new behaviors, mechanisms, and designs of biological processes relevant to DOE missions, underpinning a broader U.S. bioeconomy. By developing novel AI/ML technologies to analyze and interpret complex biological data, researchers can organize and simulate biological processes at various scales as well as advance predictive understanding and manipulation of biological systems. This integration of computation, experimentation, and next-generation experimental technologies can lead to discoveries in new biological behaviors and mechanisms relevant to DOE missions. The focus is on how advanced computational and mathematical methods can impact this mission by exploring digital twins, foundation models, automated laboratory experiments, modeling of complex living systems, and data-driven approaches for the biodesign of plants and microbial systems. While data management is important, it is not the primary focus of this workshop, which will assess the current state, trends, and AI/ML challenges at the interface between biology and computational science to identify opportunities for high-impact research at their intersection. The goal is to define research needs and opportunities that align with biological sciences, computational sciences, and applied mathematics research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dynamic, symmetry-preserving, and hardware-adaptable circuits for quantum computing many-body states and correlators of the Anderson impurity model

We present a hardware-reconfigurable ansatz on N q -qubits for the variational preparation of many-body states of the Anderson impurity model (AIM) with N imp + N bath = N q /2 sites, which conserves total charge and spin z component within each variational search subspace. The many-body ground state of the AIM is determined as the minimum over all minima of O(N$^2_ q$) distinct charge-spin sectors. Hamiltonian expectation values are shown to require ω(N q ) < N meas. $\leqslant$ O(N imp N bath ) symmetry-preserving, parallelizable measurement circuits, each amenable to postselection. To obtain the one-particle impurity Green’s function we show how initial Krylov vectors can be computed via midcircuit measurement and how Lanczos iterations can be computed using the symmetry-preserving ansatz. For a single-impurity Anderson model with a number of bath sites increasing from one to seven, we show using numerical emulation that the ease of variational ground-state preparation is suggestive of linear scaling in circuit depth and subquartic scaling in optimizer complexity. We therefore expect that, combined with time-dependent methods for Green’s function computation, our ansatz provides a useful tool to account for electronic correlations on early fault-tolerant processors. Finally, with a view towards computing real materials properties of interest like magnetic susceptibilities and electron-hole propagators, we provide a straightforward method to compute many-body, time-dependent correlation functions using a combination of time evolution, midcircuit measurement-conditioned operations, and the Hadamard test.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dynamic Cooling on Contemporary Quantum Computers

We study the problem of dynamic cooling whereby a target qubit is cooled at the expense of heating up N − 1 further identical qubits by means of a global unitary operation. A standard back-of-the-envelope high-temperature estimate establishes that the target qubit temperature can be dynamically cooled by at most a factor of 1 / N . Here we provide the exact expression for the minimum temperature to which the target qubit can be cooled and reveal that there is a crossover from the high initial temperature regime, where the scaling is 1 / N , to a low initial temperature regime, where a much faster scaling of 1 / N occurs. This slow, 1 / N scaling, which was relevant for early high-temperature NMR quantum computers, is the reason dynamic cooling was dismissed as ineffectual around 20 years ago; the fact that current low-temperature quantum computers fall in the fast, 1 / N scaling regime, reinstates the appeal of dynamic cooling today. We further show that the associated work cost of cooling is exponentially more advantageous in the low-temperature regime. We discuss the implementation of dynamic cooling in terms of quantum circuits and examine the effects of hardware noise. We successfully demonstrate dynamic cooling in a three-qubit system on a real quantum processor. Since the circuit size grows quickly with N , scaling dynamic cooling to larger systems on noisy devices poses a challenge. We therefore propose a suboptimal cooling algorithm, whereby relinquishing a small amount of cooling capability results in a drastically reduced circuit complexity, greatly facilitating the implementation of dynamic cooling on near-future quantum computers. Published by the American Physical Society2024

Physics↗
DOE OSTI2025

Towards a Quantum Algorithm for the Incompressible Nonlinear Navier-Stokes Equations

In this work, we present novel concepts for quantum algorithms to solve transient, nonlinear partial differential equations (PDEs). The challenge lies in how to effectively represent, encode, process, and evolve the nonlinear system of PDEs on quantum computers. We will discuss the new techniques using the incompressible Navier-Stokes equations as an example, because it represents the fundamental nonlinear feature and yet removes certain complexity in physics, allowing us to focus on the design of quantum algorithms. Previous attempts solving nonlinear PDEs in quantum computation have often involved storing multiple copies of solutions or employing linearizations. Neither is practical due to exponential scaling with evolution time or insufficient solution accuracy. We propose a new framework based on matrix product states (MPSs) and matrix product operators (MPOs), in addition to the Krylov subspace methods. For example, the solution variables of the Navier-Stokes equations are represented by MPSs, and the linear and nonlinear terms are processed by MPOs. The time evolution of the operators is attained by a fast-forwarding algorithm using Krylov subspace methods. Furthermore, we discuss various techniques for efficient encoding of MPSs, measurement reduction for MPOs, and use of tensor operations to treat multi-variate, multi-physics characteristics of Navier-Stokes.

Gopalakrishnan Meena, Murali [ORNL] (ORCID:0000000↗
DOE OSTI2026

ORCHA: A performance portability system for extreme heterogeneity

Heterogeneity is the prevalent trend in the rapidly evolving high-performance computing (HPC) landscape in both hardware and application software. The diversity in hardware platforms, currently comprising various accelerators and a future possibility of specializable chiplets, poses a significant challenge for scientific software developers aiming to harness optimal performance across different computing platforms while maintaining the quality of solutions when their applications are simultaneously growing more complex. Code synthesis and code generation can provide mechanisms to mitigate this challenge. We have developed a divide and conquer approach where different aspects of performance are handled by different stand-alone tools that are interfaced with the application through generated code. This portability system, ORCHA, enables users to configure and orchestrate their computations among available resources on a platform by specifying a high-level recipe, thereby permitting a many-to-many paradigm where each recipe results in a different variant of the application. The core design goal is to let users decide the application’s hardware mapping and orchestration by editing only the high-level recipe—without modifying the maintained source code or binding the application to a particular runtime system. Tools in ORCHA distribution are: CG-Kit for translating the recipe into an execution graph; Milhoja to execute the graph by orchestrating data and task movement among hardware resources; and Macroprocessor that enables users to define their own code-shorthand for higher composability and easier management of code variants. Additionally, the design of ORCHA permits tools to work in a plug-and-play mode where the application can build and run without CG-Kit and Milhoja, and either tool can be swapped out for other tools with similar capabilities by modifying the code generation portion of ORCHA. In this paper, we describe the design of ORCHA and the role that code-generation plays in isolating applications from tools. We demonstrate the breadth of configurations ORCHA enables with a case study in which an application configuration is realized on three distinct hardware mappings—a GPU-centric, a CPU/GPU balanced, and a CPU/GPU concurrent layouts by using different recipes.

Lee, Youngjun↗
DOE OSTI2025

Skyrmion-like Spin Textures Emerging in the Material Derived from Structural Frustration

Magnetic materials with complex spin textures present both fundamental and practical appeal. The complex patterns of magnetic moments emerging on underlying crystal lattices hold potential for robust information storage and processing, including the promise of topological quantum computing. The scope of materials that host such patterns, however, remains rather limited. Here, in this study, we report a discovery of a complex spin texture in a noncentrosymmetric material that emerges from the structural frustration at the boundary between centrosymmetric parent structures MnCoGe (the hexagonal Ni 2 In or the orthorhombic TiNiSi structure type) and MnCoAs (the TiNiSi structure type). Our findings demonstrate that such structural frustration provides a powerful handle for identifying compositional spaces where complex magnetic behavior and associated nontrivial magnetic structures are likely to emerge. Thus, the new phase MnCoGe 1/3 As 2/3 exhibits a modulated cycloidal antiferromagnetic arrangement of electron spins on a noncentrosymmetric lattice (of the hexagonal ZrNiAl type) that materializes in the space between centrosymmetric collinear ferromagnets. This work provides a pathway for discovering novel materials with exotic spin textures for next-generation spintronics and quantum technologies.

Wang, YiXu [Florida State University, Tallahassee,↗
DOE OSTI2026

Computationally efficient Bayesian estimation of graphical networks for omics data

Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.

EM algorithm↗
DOE OSTI2025

The Persistent Challenge of Data Locality in the Post-Exascale Era

The era of exascale computing, exemplified by systems like Frontier achieving exaflop-level performance, marks a milestone. However, the quest for sheer compute power leads to strong imbalance in system design. Hence, scaling advancements in memory, network bandwidth, and storage are also necessary and pose challenges, with a crucial need to address data locality issues. This article underscores the fundamental importance of data locality as a key abstraction for optimizing application performance. Despite notable software solutions, the growing complexity of parallelism and memory hierarchy demands performance-portable data locality solutions across diverse computing platforms. Additionally, the article revisits data locality aspects, covering hardware considerations, application perspectives, software stack abstractions, and tool support. It concludes with insights into data locality challenges and opportunities, emphasizing the ongoing significance of collaborative research for progress in this critical issue.

Unat, Didem [Koc University, Istanbul (Turkey)] (O↗