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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Unique Conductivity Behavior in Water-In-Salt Electrolytes Driven by Ion Clusters

Understanding and predicting ion transport in aqueous electrolytes are crucial for advanced energy storage and biophysics, and many emergent technologies yet remain elusive. Herein, we introduce a unified framework to quantitatively describe and predict electrolyte conductivity that shifts from conventional molar concentration-based metrics to a volume fraction-based approach. Through analyzing a variety of electrolyte solutions via this perspective, we observe a universal conductivity peak at a 37% volume fraction. Small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations reveal that nanometer-scale ion clusters drive this general behavior. Moreover, key geometric features of the ion transport pathwayssuch as pore size, tortuosity, and connectivityfollow a consistent dependence with respect to the volume fraction, reinforcing the argument for the universal conductivity trend. This paradigm shift opens new avenues for designing high-performance electrolytes and provides transformative insights for advancing studies in many fields, wherein molecular aggregates dictate transport properties.

Nguyen, Huong T. D.↗
DOE OSTI2026

Melatonin-Induced Modulation of Cholesterol-Enriched Model Neuronal Membranes

Melatonin, a hormone primarily produced by the brain’s pineal gland, not only regulates circadian rhythms, but also influences the structural and biophysical properties of neuronal membranes. Its amphiphilic nature enables direct incorporation into lipid bilayers and preferential interactions with cholesterol-rich lipid rafts, critical hubs for cellular signaling and membrane organization. Despite increasing recognition of its membrane activity, the molecular basis of melatonin’s interactions with coexisting liquid-ordered (L o ) and liquid-disordered (L d ) phases remains unclear. Here, in this study, we combine small-angle neutron scattering (SANS) and all-atom molecular dynamics simulations to examine model neuronal membranes composed of DSPC, DOPC, POPC, and cholesterol. Our results show that melatonin preserves domain morphology while adopting distinct orientations within the bilayer and at the membrane interface, allowing both lateral and transmembrane bridging across lipid phases. These findings establish the molecular underpinnings of melatonin’s modulation of membrane heterogeneity and provide strong support for its receptor-independent actions.

atomistic simulations↗
DOE OSTI2025

Metabolic skinflint or spendthrift? Insights into ground sloth integument and thermophysiology revealed by biophysical modeling and clumped isotope paleothermometry

Abstract Remains of megatheres have been known since the 18th -century and were among the first megafaunal vertebrates to be studied. While several examples of preserved integument show a thick coverage of fur for smaller ground sloths living in cold climates such as Mylodon and Nothrotheriops , comparatively very little is known about megathere skin. Assuming a typical placental mammal metabolism, it was previously hypothesized that megatheres would have had little-to-no fur as they achieved giant body sizes. Here the “hairless model of integument” is tested using geochemical analyses to estimate body temperature to generate novel models of ground sloth metabolism, fur coverage, and paleoclimate with Niche Mapper software. The simulations assuming metabolic activity akin to those of modern xenarthrans suggest that sparse fur coverage would have resulted in cold stress across most latitudinal ranges inhabited by extinct ground sloths. Specifically, Eremotherium predominantly required dense 10 mm fur with implications for seasonal changes of coat depth in northernmost latitudes and sparse fur in the tropics; Megatherium required dense 30 mm fur year-round in its exclusive range of cooler, drier climates; Mylodon and Nothrotheriops required dense 10–50 mm fur to avoid thermal stress, matching the integument remains of both genera, and further implying the use of behavioral thermoregulation. Moreover, clumped isotope paleothermometry data from the preserved teeth of four genera of ground sloth yielded reconstructed body temperatures lower than those previously reported for large terrestrial mammals (29 ± 2°–32 ± 3° C). This combination of low metabolisms and thick fur allowed ground sloths to inhabit various environments.

Deak, Michael D.↗
DOE OSTI2023

False Indications of Dose-Response Nonlinearity in Large Epidemiologic Cancer Radiation Cohort Studies; A Simulation Exercise

This study explores the likely prevalence of false indications of dose-response nonlinearity in large epidemiologic cancer radiation cohort studies (A-bomb survivors, INWORKS, Techa River). Reasons: Increasing numbers of tests of nonlinearity are being made in studies. Hypothesized nonlinear dose-response models have been justified to policy makers by analyses that rely in part on isolated findings that could be statistical fluctuations. After removing dose nonlinearity (linearization) by adjusting person-years of observation at each dose category, indications of nonlinearity, necessarily false, were counted in 5,000 randomized replications of six datasets. The average frequency of any false positive for five indicators of nonlinearity tested against a linear null was roughly 25% in Monte Carlo simulations per study, consistent with binomial calculations, increasing to ~50% within 6 studies assessed. Comparable frequencies were found using Akaike's information criterion (AIC) for model selection or multi-model averaging. False above-zero threshold doses were found more than 50% of the time, averaging to 0.05 Gy, consistent with findings in the 6 studies. Such bias, uncorrected, could distort meta-analyses of multiple studies, because meta-analyses can incorporate high P value findings. AIC-based correction for the extra threshold parameter lowered these false occurrences to 8 to 19%. Given the simulation rates, the possibility of false positives might be noted when isolated findings of nonlinearity are discussed in a regulatory context. When reporting a threshold dose with a P value > 0.05, it would be informative to note the expected high false prevalence rate due to bias.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
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 OSTI2021

Increasing large wildfires over the western United States linked to diminishing sea ice in the Arctic

Abstract The compound nature of large wildfires in combination with complex physical and biophysical processes affecting variations in hydroclimate and fuel conditions makes it difficult to directly connect wildfire changes over fire-prone regions like the western United States (U.S.) with anthropogenic climate change. Here we show that increasing large wildfires during autumn over the western U.S. are fueled by more fire-favorable weather associated with declines in Arctic sea ice during preceding months on both interannual and interdecadal time scales. Our analysis (based on observations, climate model sensitivity experiments, and a multi-model ensemble of climate simulations) demonstrates and explains the Arctic-driven teleconnection through regional circulation changes with the poleward-shifted polar jet stream and enhanced fire-favorable surface weather conditions. The fire weather changes driven by declining Arctic sea ice during the past four decades are of similar magnitude to other leading modes of climate variability such as the El Niño-Southern Oscillation that also influence fire weather in the western U.S.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor

Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Toward designing effective exascale scientific computing workflows: experiences and best practices

Many fields within scientific computing have embraced advances in big-data analysis and machine learning, which often requires the deployment of large, distributed and complicated workflows that may combine training neural networks, performing simulations, running inference, and performing database queries and data analysis in asynchronous, parallel and pipelined execution frameworks. Such a shift has brought into focus the need for scalable, efficient workflow management solutions with reproducibility, error and provenance handling, traceability, and checkpoint-restart capabilities, among other needs. Here, we discuss challenges and best-practices for deploying exascale-generation computational science workflows on resources at the Oak Ridge Leadership Computing Facility (OLCF). We present our experiences with large-scale deployment of distributed workflows on the Summit supercomputer, including for bioinformatics and computational biophysics, materials science, and deep learning model optimization. We also present problems and solutions created by working within a Python-centric software base on traditional HPC systems, and discuss steps that will be required before the convergence of HPC, AI, and data science can be fully realized. Our results point to a wealth of exciting new possibilities for harnessing this convergence to tackle new scientific challenges.

Coletti, Mark↗
DOE OSTI2022

Planar 2D wireframe DNA origami

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Semi-automated Design of Artificial Intelligence Earth Systems Models

Prediction and observation of water cycles at various scales involve not only patterns isolated in space and time, but also modeling of complex spatio-temporal relationships across multiple domains. For instance, evapotranspiration (ET) and leaf area indexes (LAI) are two parameters that are needed to accurately model and understand land-atmosphere processes. Accurate assessments of ET and LAI are critical for understanding hydrological processes, deforestation, crop yield, and irrigation impacts. However, ET estimates for global simulations are available at very coarse spatial resolution. They are usually derived from satellite data based on broad plant functional types (PFTs), which fail to capture fine-scale variations because of changes in vegetation type across the globe. Similarly LAI estimates have typically been derived from vegetation indices at global scales or estimated locally using physical models, both of which suffer from a range of uncertainties that impact model sensitivity. The new era of AI model development for Earth systems (ES) calls for data-driven methods that provide domain scientists with uncertainty-aware estimations of biophysical parameters such as ET and LAI in a generalizable, interpretable, and discoverable manner.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation

Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α) 8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. Further, the noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transmural Remodeling of Cardiac Microstructure in Aged Spontaneously Hypertensive Rats by Diffusion Tensor MRI

The long-standing high blood pressure (also known as hypertension) overworks the heart. Microstructural remodeling is a key factor of hypertensive heart disease progression. Diffusion tensor magnetic resonance imaging (DT-MRI) is a powerful tool for the rapid noninvasive nondestructive delineation of the cardiomyocyte organization. The spontaneously hypertensive rat (SHR) is a well-established model of genetic hypertension. The goal of this study was to employ high-resolution DT-MRI and the SHR animal model to assess the transmural layer-specific remodeling of myocardial microstructure associated with hypertension. Ex vivo experiments were performed on excised formalin-fixed hearts of aged SHRs (n = 4) and age-matched controls (n = 4). The DT-MRI-derived fractional anisotropy (FA), longitudinal diffusivity (λ L ), transversal diffusivity (λ T ), and mean diffusivity (MD) served as the readout parameters investigated at three transmural zones (i.e., endocardium, mesocardium, and epicardium). The helix angles (HAs) of the aggregated cardiomyocytes and the orientation of laminar sheetlets were also studied. Compared with controls, the SHRs exhibited decreased epicardial FA, while FA changes in the other two transmural regions were insignificant. No substantial differences were observed in the diffusivity parameters and the transmural course of HAs between the two groups. A consistent distribution pattern of laminar sheetlet orientation was not identified for either group. Our findings are in line with the known cellular microstructure from early painstaking histological studies. Biophysical explanations of the study outcomes are provided. In conclusion, our experimental findings indicate that the epicardial microstructure is more vulnerable to high blood pressure leading to more pronounced changes in this region during remodeling. DT-MRI is well-suited for elucidating these alterations. The revealed transmural nonuniformity of myocardial reorganization may shed light on the mechanisms of the microstructure-function relationship in hypertension progression. Our results provide insights into the management of patients with systemic arterial hypertension, thus prevent the progression toward heart failure. The findings of this study should be acknowledged by electromechanical models of the heart that simulate the specific cardiac pathology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Computational multiphysics modeling of radioactive aerosol deposition in diverse human respiratory tract geometries

The evaluation of aerosol exposure relies on generic mathematical models that assume uniform particle deposition profiles over the human respiratory tract and do not account for subject-specific characteristics. Here we introduce a hybrid-automated computational workflow that generates personalized particle deposition profiles in 3D reconstructed human airways from computed tomography scans using Computational Fluid and Particle Dynamics simulations. This is the first large-scale study to consider realistic airways variability, where 380 lower and 40 upper human respiratory tract 3D geometries are reconstructed and parameterized. The data is clustered into nine groups using random forest regression. Computational fluid and particle dynamics simulations are conducted on these representative geometries using a realistic heavy-breathing respiratory cycle and radioactive iodine-131 as a source term. Monte Carlo radiation transport simulations are performed to obtain detailed energy deposition maps. Our findings emphasize the importance of personalized studies, as minor respiratory tract variations notably influence deposition patterns rather than global parameters of the lower airways, observing more than 30% variance in the mass deposition fraction.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein- DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein–DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗