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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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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Breast Cancer Molecular Subtype as a Predictor of Radiation Therapy Fractionation Sensitivity

The predictive benefit of breast cancer molecular subtypes for systemic therapy approaches has been well established; yet, there is a paucity of data regarding their use as a predictor of radiation therapy fractionation sensitivity. The purpose of this study was to determine whether rates of local recurrence (LR) for patients treated with hypofractionated (HF) radiation therapy, in comparison to conventional fractionation, differ across breast cancer molecular subtypes in a large, prospectively collected cohort treated with modern systemic therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Processes in DNA damage response from a whole-cell multi-omics perspective

Technological advances have made it feasible to collect multi-condition multi-omic time courses of cellular response to perturbation, but the complexity of these datasets impedes discovery due to challenges in data management, analysis, visualization, and interpretation. Here, we report a whole-cell mechanistic analysis of HL-60 cellular response to bendamustine. We integrate both enrichment and network analysis to show the progression of DNA damage and programmed cell death over time in molecular, pathway, and process-level detail using an interactive analysis framework for multi-omics data. Our framework, Mechanism of Action Generator Involving Network analysis (MAGINE), automates network construction and enrichment analysis across multiple samples and platforms, which can be integrated into our annotated gene-set network to combine the strengths of networks and ontology-driven analysis. Taken together, our work demonstrates how multi-omics integration can be used to explore signaling processes at various resolutions and demonstrates multi-pathway involvement beyond the canonical bendamustine mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Additive Manufacturing with Cellulose-Based Composites: Materials, Modeling, and Applications

Recent advances in large-scale additive manufacturing (AM) with polymer-based composites have enabled efficient production of high-performance materials. Cellulose nanomaterials (CNMs) have emerged as bio-based feedstocks due to their exceptional strength and sustainability. However, challenges such as hornification and poor dispersion in polymer matrices still limit large-scale CNM–polymer composite manufacturing, requiring novel strategies. Here, this review outlines an approach starting with atomic-level simulations to link molecular composition to key parameters like bulk density, viscosity, and modulus. These simulations provide data for finite element analysis (FEA), which informs large-scale experiments and reduces the need for extensive trials. The strategy explores how atomic interactions impact the morphology, adhesion, and mechanical properties of CNM-based composites in AM processes. The review also discusses current developments in AM, along with predictions of mechanical and thermal properties for structural applications, packaging, flexible electronics, and hydrogel scaffolds. By integrating experimental findings with molecular dynamics (MD) simulations and finite element modeling (FEM), valuable insights for material design, process optimization, and performance enhancement in CNM-based AM are provided to address ongoing challenges.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Discrepancy quantification between experimental and simulated data of CO 2 adsorption isotherm using hierarchical Bayesian estimation

Here, to quantitatively analyze the inconsistencies commonly observed between experimental and simulated adsorption isotherms, parameter estimation of adsorption isotherm models was conducted by hierarchical Bayesian estimation with parameter uncertainties being quantified as probability distributions. The estimation method was implemented using Markov Chain Monte Carlo (MCMC) to analyze multiple data sets obtained from different sources, including a publicly available database. To describe the discrepancies of experimental and simulated adsorption data, the simulation data was set as the reference to which experimental measurements were compared. We applied the proposed approach to analyze CO 2 adsorption isotherms that are measured and simulated on zeolite 13X and MIL-101(Cr). In these case studies, the discrepancy of CO 2 adsorption isotherm was successfully quantified between experimental measurements and predictions given by molecular simulations using Grand Canonical Monte Carlo (GCMC), where uncertainties were quantified as probability distributions. Furthermore, experimental data sets that agree well with the GCMC simulation have been identified, providing insights into experimental and measurement methods as well as choosing the right assumptions in the molecular simulation.

42 ENGINEERING↗
DOE OSTI2022

Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development

The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO 4 ), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Exploring the impact of ions on oxygen K-edge X-ray absorption spectroscopy in NaCl solution using the GW-Bethe-Salpeter-equation approach

X-ray absorption spectroscopy (XAS) is a powerful experimental tool to probe the local structure in materials with the core hole excitations. Here, the oxygen K-edge XAS spectra of the NaCl solution and pure water are computed by using a recently developed GW-Bethe-Salpeter equation approach, based on configurations modeled by path-integral molecular dynamics with the deep-learning technique. The neural network is trained on ab initio data obtained with strongly constrained and appropriately normed density functional theory. The observed changes in the XAS features of the NaCl solution, compared to those of pure water, are in good agreement between experimental and theoretical results. We provided detailed explanations for these spectral changes that occur when NaCl is solvated in pure water. Specifically, the presence of solvating ion pairs leads to localization of electron-hole excitons. As a result, our theoretical XAS results support the theory that the effects of the solvating ions on the H-bond network are mainly confined within the first hydration shell of ions, however beyond the shell the arrangement of water molecules remains to be comparable to that observed in pure water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Modern chemical graph theory

Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods and analyses that yield qualitative and quantitative insights. Using illustrative cases within a basic mathematical framework, we showcase modern chemical graph theory's utility in Chemists' analysis and model development toolkit. The encoding of both experimental and simulation data is discussed at various levels of granularity of information. This is followed by a discussion of the two major classes of graph theoretical analyses: identifying connectivity patterns and partitioning methods. Measures, metrics, descriptors, and topological indices are then introduced with an emphasis upon enhancing interpretability and incorporation into physical models. Challenging data cases are described that include strategies for studying time dependence. Throughout, we incorporate recent advancements in computer science and applied mathematics that are propelling chemical graph theory into new domains of chemical study. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Molecular Structures

Leite, Leonardo S. G.↗
DOE OSTI2020

Mechanistic Studies of the Oxidation of Cyclohexene to 2-Cyclohexen-1-one over ALD Prepared Titania Supported Vanadia

Selective oxidation of cyclohexene to 2-cyclohexen-1-one over titania supported vanadia (VO x /TiO 2 ) has been studied using temperature dependent in-situ FTIR spectroscopy in both the presence and absence of oxygen. The VO x /TiO 2 samples were prepared using one atomic layer deposition (ALD) cycle and characterized by Raman spectroscopy. In-situ FTIR data for the oxidation of cyclohexene and perdeuterocyclohexene allow for the formulation of a molecular level reaction mechanism, which is initiated by the transfer of an allyl hydrogen. Oxidation of perdeuterocyclohexene provides a direct probe of the formation of OD and HDO moieties that support the involvement of specific steps in the proposed mechanism. The presence of gas phase oxygen does not lead to a change in the products versus anaerobic conditions. However, gas phase oxygen is significantly incorporated in the CO 2 over-oxidation product above ~250 °C. Data were also obtained with cyclohexene epoxide as the reactant in an effort to determine whether there is a parallel reaction pathway, which is initiated by C=C activation in cyclohexene, that involves cyclohexene epoxide as an intermediate. Furthermore, though a minor pathway involving a cyclohexene epoxide intermediate cannot be ruled out, these data demonstrate that, under experimental conditions, the dominant pathway from cyclohexene to cyclohexene-1-one is initiated by an allyl-H activation step and does not involve an epoxide intermediate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Physics-informed machine learning exploration of Na storage mechanisms in disordered carbon

Sodium-ion batteries are a cost-effective, sustainable alternative to lithium-ion systems for large-scale energy storage. However, optimizing sodium storage in carbon-based anodes with microstructural complexity and atomic disorder remains a major challenge. The intrinsic inhomogeneity of these materials produces diverse local environments, making it difficult for conventional methods to predict and control ion dynamics. Hard carbon (HC) anodes, composed of ranges of ordered-to-disordered graphitic and amorphous nanodomains, offer tunable ion storage and rate capacity, yet rationale design remains a challenge due to poorly understood correlation between local atomic feature and ion transport mechanism. Here, to address this challenge, we introduce a data-driven framework that integrates validated machine-learned interatomic potentials, large-scale molecular dynamics simulations, and machine learning to elucidate sodium transport mechanisms as a function of carbon and sodium loading densities. By computing per-ion structural descriptors and applying unsupervised learning, we identify distinct diffusion modes governed by microscopic features. Supervised analysis and correlation mapping then establish quantitative links between these transport regimes and processing variables such as bulk carbon density and sodium content. This physics-informed approach establishes quantitative structure–transport relationships and offers actionable design principles for engineering high-performance HC anodes.

Data-driven framework↗
DOE OSTI2022

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Science & Technology - Other Topics↗
DOE OSTI2022

Temporal Study 2021-2022: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of temporal variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected at weekly or bi-weekly intervals at six sites across the Yakima River Basin in Washington, USA. Related sensor data will be published separately and can be used to link sediment respiration rates to biogeochemical processing rates. The data package was originally published in November 2022. It was updated in November 2023 (v2; modified files) and April 2025 (new and modified files). See the change history section in readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), and ions; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol; (8) readme; (9) methods codes; (10) international generic sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected our data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Revealing Site Occupancy in a Complex Oxide: Terbium Iron Garnet

Complex oxide films stabilized by epitaxial growth can exhibit large populations of point defects which have important effects on their properties. The site occupancy of pulsed laser-deposited epitaxial terbium iron garnet (TbIG) films with excess terbium (Tb) is analyzed, in which the terbium:iron (Tb:Fe)ratio is 0.86 compared to the stoichiometric value of 0.6. The magnetic properties of the TbIG are sensitive to site occupancy, exhibiting a higher compensation temperature (by 90 K) and a lower Curie temperature (by 40 K) than the bulk Tb 3 Fe 5 O 12 garnet. Data derived from X-ray core-level spectroscopy, magnetometry, and molecular field coefficient modeling are consistent with occupancy of the dodecahedral sites by Tb 3+ , the octahedral sites by Fe 3+ , Tb 3+ and vacancies, and the tetrahedral sites by Fe 3+ and vacancies. Energy dispersive X-ray spectroscopy in a scanning transmission electron microscope provides direct evidence of Tb Fe antisites. A small fraction of Fe 2+ is present, and oxygen vacancies are inferred to be present to maintain charge neutrality. In conclusion, variation of the site occupancies provides a path to considerable manipulation of the magnetic properties of epitaxial iron garnet films and other complex oxides, which readily accommodate stoichiometries not found in their bulk counterparts.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Impact of humidity on gas transport in polybenzimidazole membranes

Polybenzimidazoles (PBIs) are promising materials for high temperature H 2 /CO 2 separation in applications such as steam reforming and pre-combustion carbon capture where significant amounts of water are often present. However, PBIs are hydrophilic, and the impact of humidity on PBI gas separation properties is relatively unexplored. Furthermore, opportunity exists to elucidate the interplay between plasticization, free volume, and gas transport in glassy polymer membranes such as PBIs. Here, this study investigates the effect of humidity on H 2 , O 2 , and CO 2 permeabilities at 35 °C in a commercial PBI and two sulfone-containing PBIs. Water uptake significantly reduces PBI gas permeabilities at low humidities due to competitive sorption and antiplasticization. At high humidities, plasticization increases the permeabilities of larger gases in more hydrophilic PBIs. Effective fractional free volumes evaluated from gas permeation data and previously reported water sorption and dilation data suggest water plasticizes PBIs by increasing accessible free volume via enhanced molecular dynamics rather than by creating new free volume cavities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Deep Learning Approaches for Predicting the Surface Tension of Ionic Liquids

Ionic liquids (ILs) are a novel class of solvents that have attracted significant attention due to their unique and tunable properties. Among their physiochemical characteristics, surface tension plays a critical role in various industrial applications including electrolytes, heat transfer fluids, and separation processes. However, because of the exploratory nature of IL design and the vast combinatorial space of possible anion–cation pairs, the experimental determination of these properties is often impractical, being both time-consuming and costly. To overcome these challenges, computational approaches are increasingly employed to develop accurate predictive models that can accelerate IL discovery and design. In this study, we present two deep learning (DL) models for predicting the surface tension of ILs across a broad temperature range at a constant pressure. The models use simplified molecular input line entry system, SMILES, representations of ILs to extract molecular features as inputs. Both DL models demonstrate excellent agreement with experimental data, achieving an R 2 value of 0.990 and a root-mean-square error of 0.792 mN/m. In conclusion, these results offer valuable insights for the rapid screening and rational design of ILs with tailored surface tension values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond

Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Multiscale Modeling and Experimental Insights into High-Temperature Soil Biodegradation Dynamics of Semi-Crystalline Poly(Lactic Acid) Nonwoven Fabrics

This study investigates the biodegradation of semi-crystalline poly(lactic acid) (PLA) nonwovens (NWs) in soil at 58 °C using both experimental and mathematical modeling approaches. The model utilizes a system of parabolic diffusion-reaction partial differential equations (PDEs) to elucidate chemical transformations over time and in space. It accounts for phenomena such as the diffusion of water and lactic acid monomers through the polymer matrix and into the surrounding soil, along with their microbial breakdown. It also accounts for the initial PLA crystallinity and predicts its evolution in time. The model is solved numerically for a single filament, and the results were used to shed light on PLA NW transformations observed in soil over a 180-day incubation period. Various characterization techniques, including scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and Raman spectroscopy, were employed to assess morphological changes, crystallinity, and molecular changes in the NWs throughout the experiment. By comparing the experimental data with the model predictions, the hydrolysis rate coefficient was found to be 3.37 × 10 -7 s -1 , while the rate of microbial degradation of lactic acid monomers was faster, of the order of 9.63 × 10 -7 s -1 . The findings highlight the significant role of crystallinity in the biodegradation process. The PLA degradation ceases when no amorphous material remains, and the crystallinity reaches 0.8, as observed in the experiments by day 120. Furthermore, this research contributes to a deeper understanding of PLA biodegradation dynamics and offers insights for effectively managing biodegradable materials in environmental settings.

Diffusion−reaction modeling↗
DOE OSTI2022

Atomic-Layer-Deposited Aluminum Oxide Thin Films Probed with X-ray Scattering and Compared to Molecular Dynamics and Density Functional Theory Models

A better understanding of amorphous aluminum oxide’s structure and electronic properties is obtained through combined experimental and computational approaches. Grazing incidence X-ray scattering measurements were carried out on aluminum oxide thin films grown using thermal atomic layer deposition. The corresponding pair distribution functions (PDFs) showed structures similar to previously reported PDFs of solid-state amorphous alumina and molten alumina. Structural models based on crystalline alumina polymorphs (PDFgui) and amorphous alumina (molecular dynamics, MD) were examined for structural comparisons to the experimental PDF data. Smaller MD models were optimized and verified against larger models to allow for quantum chemical electronic structure calculations. The electronic structure of the amorphous alumina models yields additional insight into the band structure and electronic defects present in amorphous alumina that are not present in crystalline samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗