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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamic in-context learning with conversational models for data extraction and materials property prediction

The advent of natural language processing and large language models (LLMs) has revolutionized the extraction of data from unstructured scholarly papers. However, ensuring data trustworthiness remains a significant challenge. In this paper, we introduce PropertyExtractor, an open-source tool that leverages advanced conversational LLMs such as Google gemini-pro and OpenAI gpt-4, blends zero-shot with few-shot in-context learning, and employs engineered prompts for the dynamic refinement of structured information hierarchies—enabling autonomous, efficient, scalable, and accurate identification, extraction, and verification of material property data. Our tests on material data demonstrate precision and recall that exceed 95% with an error rate of ∼9%, highlighting the effectiveness and versatility of the toolkit. Finally, databases for 2D material thicknesses, a critical parameter for device integration, and energy bandgap values are developed using PropertyExtractor. In particular, for the thickness database, the rapid evolution of the field has outpaced both experimental measurements and computational methods, creating a significant data gap. Our work addresses this gap and showcases the potential of PropertyExtractor as a reliable and efficient tool for the autonomous generation of various material property databases, advancing the field.

Ekuma, Chinedu E. (ORCID:0000000258527556)↗
DOE OSTI2026

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗
DOE OSTI2026

Perspective of Fermi’s golden rule and its generalizations in chemical physics

This perspective provides a succinct history of Fermi’s golden rule (FGR), an overview of its derivation, assumptions, and representative forms. Major applications of FGR, mostly in the field of chemical physics, are reviewed. These illustrate the broad applicability and success of FGR. Ambiguities and open issues encountered in practical applications of FGR are clarified. Recent advances in generalizations of FGR and computational methods for practical applications are addressed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Linear resistivity and Sachdev-Ye-Kitaev (SYK) spin liquid behavior in a quantum critical metal with spin-1/2 fermions

Significance In “Planckian metals,” electrons dissipate energy at the fastest possible rate allowed by the fundamental laws of quantum mechanics, resulting in a linear temperature dependence of their electrical resistivity. Although observed for a number of quantum materials, this phenomenon lacks a general theoretical understanding and is often considered as one of the prominent fundamental questions in condensed matter physics. Here, we show that Planckian dissipation and a behavior consistent with the “marginal Fermi liquid” phenomenology emerge in the quantum critical regime separating a Mott insulating spin glass and a Fermi liquid. By establishing this behavior in an explicit model solvable by state-of-the-art computational methods, our theory paves the way toward a deeper understanding of Planckian or “strange” metals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Protein folds vs. protein folding: Differing questions, different challenges

We report protein fold prediction using deep-learning artificial intelligence (AI) has transformed the field of protein structure prediction. By combining physical and geometric constraints—and especially patterns extracted from the Protein Data Bank —these machine learning algorithms can predict protein structures at or near atomic resolution and do so in seconds. Today, these computational methods have now solved more than 200 million protein structures, which are accessible from the AlphaFold Protein Structure Database. This accomplishment seems all the more remarkable because few thought it possible or saw it coming. Deservedly, deep-learning AI was named Science magazine’s 2021 “breakthrough of the year”. Clearly, deep-learning AI represents a major advance in protein fold prediction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Extending the Nuclide Inventory Validation Basis for High-Burnup Fuel with New Radiochemical Assay Data

Efforts are underway at Oak Ridge National Laboratory to improve the nuclide inventory validation basis for spent nuclear fuel at high burnups. Recently conducted radiochemical assay experiments provided new measurement data for nine samples of fuel irradiated in a pressurized water reactor, with estimated sample burnups in the 30 to 70 GWd/t range. This type of destructive assay data is essential for validating computational methods, tools, and nuclear data applied in nuclear safety analyses and for improving our understanding of the bias and uncertainty in code predictions. The measurement data include key actinides and fission products that span a gamut of needs and interests for nuclear science and engineering applications in criticality safety, reactor physics, nuclide inventory, decay heat, and radiation shielding. The SCALE 6.3 code system with ENDF/B-VII.1 cross-section libraries was used to simulate the irradiation histories of the measured fuel samples. The calculated nuclide concentrations are compared to corresponding measurement data. The significance of the comparisons is discussed, emphasizing how the addition of the new measurement data fills gaps in the validation basis at high burnups and contributes to the decrease in bias and uncertainty for predicted nuclide concentrations. The discussion addresses the effect of the sample burnup used in the simulation—which is based on reactor operator records or on calibration to measured data for burnup indicator fission products—on the validation results.

Nuclide inventory↗
DOE OSTI2026

Transition Metals Separation with Commercial Neutral Extractants – A Review

The increasing use of extraction chromatography resins across fields such as hydrometallurgy, nuclear medicine, and environmental analysis has created a need for a deeper understanding of their interactions with transition metals. Despite extensive research on f-element separations, the behavior of transition metals in these systems remains relatively understudied. This review provides a comprehensive overview of the current state of knowledge on the extraction behavior of transition metals with neutral extractants, including TODGA, TEHDGA, TBP, and CMPO, and their corresponding resins, such as DGA, BDGA, UTEVA, TBP, and TRU. The review summarizes extraction data, extracted complex coordination environments, separation reaction stoichiometries, and associated thermodynamics, highlighting inconsistencies and knowledge gaps in the literature. The study emphasizes the need for further research using spectroscopy and computational methods to elucidate extraction mechanisms and to improve the efficiency and selectivity of transition metal separations. By identifying areas for future research and development, this review aims to stimulate advancements in the field and promote the development of innovative separation technologies. The implications of this research are far-reaching, with potential applications in nuclear waste management, nuclear forensics, metal recovery, and environmental remediation. Overall, this review provides a foundation for future studies on the extraction of transition metals using neutral extractants and resins.

Wall, Nathalie A.↗
DOE OSTI2024

Physics-informed neural networks for heterogeneous poroelastic media

This study presents a novel physics-informed neural network (PINN) framework for modeling poroelasticity in heterogeneous media with material interfaces. The approach introduces a composite neural network (CoNN) where separate neural networks predict displacement and pressure variables for each material. While sharing identical activation functions, these networks are independently trained for all other parameters. To address challenges posed by heterogeneous material interfaces, the CoNN is integrated with the Interface-PINNs (I-PINNs) framework (Sarma et al., Comput. Methods Appl. Mech. Eng. 429: 117135, 2024), allowing different activation functions across material interfaces. Further, this ensures accurate approximation of discontinuous solution fields and gradients. Performance and accuracy of this combined architecture were evaluated against the conventional PINNs approach, a single neural network (SNN) architecture, and the eXtended PINNs (XPINNs) framework through two one-dimensional benchmark examples with discontinuous material properties. The results show that the proposed CoNN with I-PINNs architecture achieves an RMSE that is two orders of magnitude better than the conventional PINNs approach and is at least 40 times faster than the SNN framework. Compared to XPINNs, the proposed method achieves an RMSE at least one order of magnitude better and is 40% faster.

42 ENGINEERING↗
DOE OSTI2023

Electronic signatures of successive itinerant, antiferromagnetic transitions in hexagonal La 2 Ni 7

We use high-resolution angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT) calculations to study the electronic and magnetic properties of La 2 Ni 7 , an itinerant magnetic system with a series of three magnetic transition temperatures upon cooling, which end in a small moment antiferromagnetic (smAFM) ground state. Our APRES data reveal several electron and hole pockets that have hexagonal symmetry near the Γ point. We observe significant reconstruction of the band structure upon successive magnetic transitions at T 1 ~ 61 K, T 2 ~ 57 K and T 3 ~ 42 K. Several features observed in ARPES data were reasonably well reproduced by DFT calculations, while others were not. In particular, the flat band near E f predicted by DFT in AFM state, was seemingly absent in ARPES data. Our results detail the effects of magnetic ordering on the electronic structure in a Ni-based small moment antiferromagnet and highlight challenges of current computational methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A probabilistic-phase field model for the fracture of brittle materials

Abstract We develop a computational method to determine the failure probability of brittle materials under general mechanical loading conditions. The method is a combination of two parts: (1) numerical simulations of materials with multiple cracks using phase field theory, where the complete fracture process is viewed as ‘damage percolation’ along critical paths or clusters of cracks, rather than the traditional weak-link failure mechanism of Weibull, and (2) an extension of the Batdorf statistical theory of fracture to finite domains, where it is implemented within the finite element framework. The results of phase-field simulations at the ‘percolation threshold’ are used as failure data in the Batdorf theory to determine the overall probability of failure. The input to this approach is the size distribution of cracks in a pristine material. An example is shown, where alumina samples that were previously tested by Abe and coworkers (Abeet al2003J. Am. Ceram. Soc.861019–21) in four-point loading are compared to the results of our numerical simulations. The approach developed here has the advantage of being extendable to more complex thermomechanical loading.

Materials Science↗
DOE OSTI2022

Fundamentals of hydrogen storage in nanoporous materials

Abstract Physisorption of hydrogen in nanoporous materials offers an efficient and competitive alternative for hydrogen storage. At low temperatures (e.g. 77 K) and moderate pressures (below 100 bar) molecular H 2 adsorbs reversibly, with very fast kinetics, at high density on the inner surfaces of materials such as zeolites, activated carbons and metal–organic frameworks (MOFs). This review, by experts of Task 40 ‘Energy Storage and Conversion based on Hydrogen’ of the Hydrogen Technology Collaboration Programme of the International Energy Agency, covers the fundamentals of H 2 adsorption in nanoporous materials and assessment of their storage performance. The discussion includes recent work on H 2 adsorption at both low temperature and high pressure, new findings on the assessment of the hydrogen storage performance of materials, the correlation of volumetric and gravimetric H 2 storage capacities, usable capacity, and optimum operating temperature. The application of neutron scattering as an ideal tool for characterising H 2 adsorption is summarised and state-of-the-art computational methods, such as machine learning, are considered for the discovery of new MOFs for H 2 storage applications, as well as the modelling of flexible porous networks for optimised H 2 delivery. The discussion focuses moreover on additional important issues, such as sustainable materials synthesis and improved reproducibility of experimental H 2 adsorption isotherm data by interlaboratory exercises and reference materials.

08 HYDROGEN↗
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗
DOE OSTI2025

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Ludwig, David W↗
DOE OSTI2020

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗