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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Liquid Structure and Transport Properties of the Deep Eutectic Solvent Ethaline

A range of techniques including physical property measurements, neutron scattering experiments, ab initio molecular dynamics, and classical molecular dynamics simulations are used to probe the structural, thermodynamic, and transport properties of a deep eutectic solvent comprised of a 1:2 molar ratio of choline chloride and ethylene glycol. This mixture, known as Ethaline, has many desirable properties for use in a range of applications, and therefore, understanding its liquid structure and transport properties is of interest. Simulation results are able to capture experimental densities, diffusivities, viscosities, and structure factors extremely well. Here, the solvation environment is dynamic and dominated by different hydrogen bonding interactions. Dynamic heterogeneities resulting from hydrogen bonding interactions are quantified. Rotational dynamics of molecular dipole moments of choline and ethylene glycol are computed and found to exhibit a fast and slow mode.

25 ENERGY STORAGE↗
DOE OSTI2020

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver. Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Global Data-Driven Determination of Baryon Transition Form Factors

Hadronic resonances emerge from strong interactions encoding the dynamics of quarks and gluons. The structure of these resonances can be probed by virtual photons parametrized in transition form factors. Here, in this study, twelve N* and Δ transition form factors at the pole are extracted from data with the center-of-mass energy from πN threshold to 1.8 GeV, and the photon virtuality 0 ≤ Q 2 /GeV 2 ≤ 8. For the first time, these results are determined from a simultaneous analysis of more than one state, i.e., ~10 5 π⁢N, η⁢N, and K⁢Λ electroproduction data. In addition, about 5×10 4 data in the hadronic sector as well as photoproduction serve as boundary conditions. For the Δ⁡(1232) and N⁡(1440) states our results are in qualitative agreement with previous studies, while the transition form factors at the poles of some higher excited states are estimated for the first time. Realistic uncertainties are determined by further exploring the parameter space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Structure and conformational dynamics of Clostridioides difficile toxin A

Clostridioides difficile toxin A and B (TcdA and TcdB) are two major virulence factors responsible for diseases associated with C. difficile infection (CDI). Here, we report the 3.18-Å resolution crystal structure of a TcdA fragment (residues L843–T2481), which advances our understanding of the complete structure of TcdA holotoxin. Our structural analysis, together with complementary single molecule FRET and limited proteolysis studies, reveal that TcdA adopts a dynamic structure and its CROPs domain can sample a spectrum of open and closed conformations in a pH-dependent manner. Furthermore, a small globular subdomain (SGS) and the CROPs protect the pore-forming region of TcdA in the closed state at neutral pH, which could contribute to modulating the pH-dependent pore formation of TcdA. A rationally designed TcdA mutation that trapped the CROPs in the closed conformation showed drastically reduced cytotoxicity. Taken together, these studies shed new lights into the conformational dynamics of TcdA and its roles in TcdA intoxication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Correlating Protein Dynamics and Catalytic Activity of a Model Hydrogenase Using Paramagnetic and Biological Nuclear Magnetic Resonance Spectroscopy

Rational catalyst design remains a significant challenge, with electronic structure, steric, and electrostatic effects known to contribute to activity. Recently, dynamics has been recognized as another factor that impacts catalysis, though identifying and predicting these effects has remained out of reach. Nickel-substituted rubredoxin (NiRd), a protein-based mimic of a hydrogenase enzyme, serves as a model catalytic system in which dynamics can be systematically investigated with respect to activity. While over 30 secondary-sphere mutants of NiRd have been shown to be catalytically active, no significant correlation was observed between the rates and catalytic overpotential or electronic structure, prompting questions about the protein-derived factors that modulate activity. Here, in this work, NMR spectroscopy was used to investigate the roles of substrate accessibility, protein dynamics, and protein stability in controlling catalysis. Significant paramagnetic effects from the nickel center (S = 1) isolate the methylene proton resonances of the metal-coordinating cysteine residues. The sensitivity of resonance positions and linewidths to local environment offers an opportunity to study dynamical molecular changes around the metal center with high resolution. Machine learning algorithms were employed to identify correlations between the catalytic activity and the paramagnetic NMR spectra. These analyses revealed spectroscopic features of specific cysteine protons that report on catalytic overpotential and increased turnover rates, which are further supported by the results obtained using high-field NMR techniques. Collectively, these studies indicate the potential for multifrequency NMR techniques to resolve key contributors to catalytic activity and highlight the importance of local and outer-sphere dynamics.

Protein Engineering↗
DOE OSTI2022

Disentangling multiple scattering with deep learning: application to strain mapping from electron diffraction patterns

Abstract A fast, robust pipeline for strain mapping of crystalline materials is important for many technological applications. Scanning electron nanodiffraction allows us to calculate strain maps with high accuracy and spatial resolutions, but this technique is limited when the electron beam undergoes multiple scattering. Deep-learning methods have the potential to invert these complex signals, but require a large number of training examples. We implement a Fourier space, complex-valued deep-neural network, FCU-Net, to invert highly nonlinear electron diffraction patterns into the corresponding quantitative structure factor images. FCU-Net was trained using over 200,000 unique simulated dynamical diffraction patterns from different combinations of crystal structures, orientations, thicknesses, and microscope parameters, which are augmented with experimental artifacts. We evaluated FCU-Net against simulated and experimental datasets, where it substantially outperforms conventional analysis methods. Our code, models, and training library are open-source and may be adapted to different diffraction measurement problems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Specific Ion Solvation and Pairing Effects in Glycerol Carbonate

Identifying the driving forces behind the solvation of inorganic salts by nonaqueous solvents is an important step in the development of green solvents. Here we focus on one promising solvent: glycerol carbonate (GC). Using ab initio molecular dynamics simulations, we build upon our previous work by detailing glycerol carbonate’s interactions with a series of anions, a lithium ion, and the LiF ion pair. Through these investigations, we highlight the changes in solvation behavior as the anion size increases, the competition of binding shown by lithium for the oxygens of GC, and the behavior of the LiF ion pair in a GC solution. These results in this work indicate the importance of the cation’s identity in ion-pairing structure and dynamics and lend insight into the key factors behind the specific ion effects seen in GC.

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

Evolution of Charge-Lattice Dynamics across the Kuramoto Synchronization Phase Diagram of Quantum Tunneling Polarons in Cuprate Superconductors

Because of its sensitivity to the instantaneous structure factor, S(Q,t = 0), Extended X-ray Absorption Fine Structure (EXAFS) is a powerful tool for probing the dynamic structure of condensed matter systems in which the charge and lattice dynamics are coupled. When applied to hole-doped cuprate superconductors, EXAFS has revealed the presence of internal quantum tunneling polarons (IQTPs). An IQTP arises in EXAFS as a two-site distribution for certain Cu–O pairs, which is also duplicated in inelastic scattering but not observed in standard diffraction measurements. The Cu–Sr pair distribution has been found to be highly anharmonic and strongly correlated to both the IQTPs and to superconductivity, as, for example, in YSr 2 Cu 2.75 Mo 0.25 O 7.54 (T c =84 K). In order to describe such nontrivial, anharmonic charge-lattice dynamics, we have proposed a model Hamiltonian for a prototype six-atom cluster, in which two Cu-apical-O IQTPs are charge-transfer bridged through Cu atoms by an O atom in the CuO 2 plane and are anharmonically coupled via a Sr atom. By applying an exact diagonalization procedure to this cluster, we have verified that our model indeed produces an intricate interplay between charge and lattice dynamics. Then, by using the Kuramoto model for the synchronization of coupled quantum oscillators, we have found a first-order phase transition for the IQTPs into a synchronized, phase-locked phase. Most importantly, we have shown that this transition results specifically from the anharmonicity. Finally, we have provided a phase diagram showing the onset of the phase-locking of IQTPs as a function of the charge-lattice and anharmonic couplings in our model. We have found that the charge, initially confined to the apical oxygens, is partially pumped into the CuO 2 plane in the synchronized phase, which suggests a possible connection between the synchronized dynamic structure and high-temperature superconductivity (HTSC) in doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Temperature-induced gradual polymorphic structural crossover in liquid indium, tin, and antimony

Temperature-induced polymorphic structural crossover in metallic liquid indium (In), tin (Sn), and antimony (Sb) is investigated by in situ high-energy x-ray diffraction and ab initio molecular dynamics simulations. The results demonstrate the existence of a temperature-induced reversible and gradual structural crossover in these three liquids, reflecting from both “static” structures, e.g., peak positions of the structure factor and pair distribution function, bond angle distribution, number of tetrahedra, cluster connection, free volume, and dynamical behaviors, including the relaxation time, diffusion coefficient, and non-Gaussian parameter. Further, the main difference from liquid In, Sn, to Sb is that not only the large-sized free volume but also the anharmonicity and the dynamical heterogeneity increase significantly with the appearance of strong covalent bonds. These findings will deepen the understanding of liquid structure and the liquid-liquid transition in metallic liquids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Determining the influence of temperature and pressure on the structural stability in a polyurea elastomer

The structural response of amorphous elastomers to applied pressure and temperature is of significant interest given their potential for blast and impact protection applications. While understanding disordered structures is often challenging, this study focuses on the ordered correlations that are present at the atomic level even in amorphous materials. This local order was characterized in polyurea elastomers with two molecular weights up to 6 GPa and ~280 °C using in situ energy dispersive X-ray diffraction at the Advanced Photon Source via total scattering techniques. The resulting structure factors and pair distribution functions indicate that the applied pressure reduced the free volume but had little effect on covalent bonds for both molecular weights. Temperature-induced order-disorder transitions that occur readily at ambient pressures within the temperature range studied here were not observed, their onset likely delayed by the limited chain mobility associated with the free volume reduction. In conclusion, this study demonstrates that total scattering offers insights into the high-pressure structure of disordered polymers that are otherwise inaccessible using more conventional X-ray scattering techniques.

42 ENGINEERING↗
DOE OSTI2024

Complex Structure of Molten FLiBe (2 Li F – Be F 2 ) Examined by Experimental Neutron Scattering, X-Ray Scattering, and Deep-Neural-Network Based Molecular Dynamics

The use of molten salts as coolants, fuels, and tritium breeding blankets in the next generation of fission and fusion nuclear reactors benefits from furthering the characterization of the molecular structure of molten halide salts, paving the way to predictive capability of the chemical and thermophysical properties of molten salts. Due to its neutronic, chemical, and thermochemical properties, 2 Li F - Be F 2 is a candidate molten salt for several fusion- and fission-reactor designs. We performed neutron and x-ray total-scattering measurements to determine the atomic structure of liquid 2 Li F - Be F 2 . We also performed and neural-network molecular-dynamics simulations to predict the structure obtained by neutron- and x-ray-diffraction experiments. The use of machine learning provides improvements to the efficiency in predicting the structure at a longer length scales than is achievable with simulations at significantly lower computational expense while retaining near accuracy. We found that the NNMD simulations accurately predicted the Be F 4 2 − oligomer formations seen in the experimental first-structure-factor peak. Our combination of high-resolution measurements with large-scale molecular dynamics provided an avenue to explore and experimentally verify the intermediate-range ordering beyond the first-nearest neighbor that has posed too many experimental and computational challenges in previous works. With a deeper understanding of the salt structure and ion ordering, the evolution of salt chemistry over the lifetime of a reactor can be better predicted, which is crucial to the licensing and operation of advanced fission and fusion reactors that employ molten salts. To this end, this work will serve as a reference for future studies of salt structure and macroscopic properties with and without the addition of solutes. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Self-Assembled Solute Networks in Crowded Electrolyte Solutions and Nanoconfinement of Charged Redoxmer Molecules

Redoxmers are electrochemically active organic molecules storing charge and energy in electrolyte fluids circulating through redox flow batteries (RFBs). Such molecules typically have solvent-repelling cores and solvent-attracting pendant groups introduced to increase solubility in liquid electrolytes. These two features can facilitate nanoscale aggregation of the redoxmer molecules in crowded solutions. In some cases, this aggregation leads to the emergence of continuous networks of solute molecules in contact, and the solution becomes microscopically heterogeneous. In this study, we used small-angle X-ray scattering (SAXS) and molecular dynamics modeling to demonstrate formation of such networks and examine structural factors controlling this self-assembly. We also show that salt ions become excluded from these solute aggregates into small pockets of electrolytes, where these ions strongly associate. This confinement by exclusion is also likely to occur to charged redoxmer molecules in a “sea” of neutral precursors coexisting in the same solution. Here, we demonstrate that the decay lifetime of the confined charged molecules in such solutions can increase several fold compared to dilute solutions. We attribute this behavior to a “microreactor effect” on reverse reactions of the confined species during their decomposition.

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

Evaluating ecosystem water use efficiency under drought stress: a case study of the Helan Mountain region, northwest China

Context Water use efficiency (WUE) is a fundamental ecological indicator links carbon assimilation and water loss in terrestrial ecosystems. Understanding its responses to drought stress is essential for adaptive ecosystem management, particularly in climate-sensitive mountain landscapes. Objectives This study aimed to investigate drought-driven variations in WUE across major vegetation types in the Helan Mountain region of Northwest China. Specifically, we sought to identify dominant ecological drivers of WUE variability and to disentangle their relative importance and causal pathways. Methods We quantified WUE using the Moderate Resolution Imaging Spectroradiometer (MODIS) products and the Drought Severity Index (DSI) data from 2001 to 2020. To examine WUE – drought relationships across contrasting vegetation types, we employed a spatially explicit analytical framework integrating Random Forest (RF) modeling, partial correlation analysis, and structural equation modeling (SEM). Results Regional WUE exhibited relatively stable interannual dynamics, yet pronounced spatial heterogeneity that was strongly modulated by drought conditions. Vegetation properties, particularly Leaf Area Index (LAI) and Normalized Difference Vegetation Index (NDVI), emerged as the dominant determinants of WUE, with NDVI alone explaining over 20% of its spatial variance in forest and grassland during non-drought periods. SEM analyses revealed that climate forcing influenced WUE mainly through indirect pathways mediated by soil moisture availability and vegetation structural dynamics, rather than through direct climatic controls. Among all regulating factors, LAI acted as the central control node governing ecosystem carbon–water coupling. In contrast, short-term climatic stress, especially atmospheric demand and drought duration, exerted weak or negative direct effects on WUE. Ecosystem-specific responses were observed, with croplands mainly regulated by soil water availability, whereas forests and grasslands showed more sensitive to atmospheric drought stress. Together, these results reveal a hierarchical control framework where soil–vegetation interactions mediate climate impacts on WUE, driving strong spatial heterogeneity in drought responses across mountain landscapes. Conclusions Our findings highlight the pivotal role of indirect drought effects mediated by vegetation and soil processes in shaping ecosystem WUE. The identified soil–vegetation–climate regulatory hierarchy provides mechanistic insight into landscape–scale drought sensitivity and supports integrated modeling approaches for evaluating ecosystem resilience and sustainable management in arid mountain regions.

China↗
DOE OSTI2024

Salt matters: How ionic strength and electrolytes impact redox polymer reactivity and dynamics for energy storage

As the global demand for sustainable energy grows, redox-active polymers (RAPs) have emerged as promising materials for batteries due to their advantages in stability, ease of preparation, and low-cost processability. Despite factors traditionally known to impact polymer dynamics (e.g., temperature, viscosity, and structure), we posit that investigating the effect of ionic strength and/or supporting electrolyte types on the electrochemical performance of RAP systems is crucial, both in aqueous and nonaqueous systems. Here, we first highlight recent findings on RAP-electrolyte interactions, elucidating how their polyelectrolyte nature determines their redox activity. Then, we focus on strategies to enhance RAP performance for energy storage through ionic strength optimization and tailored electrolyte composition. These insights into the modulation of RAP reactivity provide a foundation for improving battery performance in both flow and stationary configurations, thus facilitating progress toward next-generation energy storage solutions.

25 ENERGY STORAGE↗
DOE OSTI2023

Characterizing the Mechanisms of Ca and Mg Carbonate Ion-Pair Formation with Multi-Level Molecular Dynamics/Quantum Mechanics Simulations

The carbonate minerals of Ca and Mg are abundant throughout the lithosphere and have recently garnered significant research interest as possible long-term carbon sinks in the sequestration of atmospheric carbon dioxide. Nonetheless, an understanding of the atomic-level processes comprising their mineralization remains limited. Furthermore, we characterize and contrast the mechanisms of contact ion-pair formation in aqueous Ca and Mg carbonate systems, which represents the most fundamental step leading to the formation of their mineral solids. Utilizing multilevel embedded correlated wavefunction-based ab initio molecular dynamics/quantum mechanics simulations, we characterize not only the dynamics of these processes but also factors arising from the electronic structure of the involved species, revealing further details of the fundamentally different mechanisms for the interconversion between the contact ion-pairs and solvent-shared ion-pairs of Ca versus Mg carbonate.

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

Unraveling the Heterogeneous but Ordered Microstructure of the Nonionic Deep Eutectic Solvent Formed by Lauric Acid and N -Methylacetamide

The nonionic deep eutectic solvent, formed by lauric acid (LA) and N-methylacetamide (NMA), has been shown to have a heterogeneous molecular structure in which the LA and NMA form nonpolar and polar domains, respectively. Previous vibrational spectroscopy experiments demonstrated that the ability of the LA domains to solvate compounds was limited to long carbon chains, whereas other nonpolar molecules, such as W(CO) 6 , were found to be solvated by both LA and NMA. These experiments were not fully compatible with the previously proposed micelle-like structure of the nonpolar domains of the LA-NMA DES. In this work, the modeling of the DES molecular structure is pursued using classical molecular dynamics simulations. The new classical model reproduces both the SAXS structural factors and the previously experimentally derived interaction map for these LA-NMA DESs. In addition, the simulation also shows that LA-NMA DESs form highly organized LA aggregates that are difficult to disorganize. Further evidence of the correct description provided by the newly derived model is obtained using a moderately polar probe: chloroform-d. Computations using the classical model have a good agreement with the solvation behavior of the probe derived from experiments, in which the location of the probe is found to be mostly within the polar domain of the DES. The computational model also demonstrates that the probe solvation is a consequence of the tightly packed LA structure, which causes nonpolar molecules to be located at the interphase of the DES nonpolar domains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗