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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 OSTI2024

A Novel Non‐Destructive Rapid Tool for Estimating Amino Acid Composition and Secondary Structures of Proteins in Solution

Abstract Amino‐acid protein composition plays an important role in biology, medicine, and nutrition. Here, a groundbreaking protein analysis technique that quickly estimates amino acid composition and secondary structure across various protein sizes, while maintaining their natural states is introduced and validated. This method combines multivariate statistics and the thermostable Raman interaction profiling (TRIP) technique, eliminating the need for complex preparations. In order to validate the approach, the Raman spectra are constructed of seven proteins of varying sizes by utilizing their amino acid frequencies and the Raman spectra of individual amino acids. These constructed spectra exhibit a close resemblance to the actual measured Raman spectra. Specific vibrational modes tied to free amino and carboxyl termini of the amino acids disappear as signals linked to secondary structures emerged under TRIP conditions. Furthermore, the technique is used inversely to successfully estimate amino acid compositions and secondary structures of unknown proteins across a range of sizes, achieving impressive accuracy ranging between 1.47% and 5.77% of root mean square errors (RMSE). These results extend the uses for TRIP beyond interaction profiling, to probe amino acid composition and structure.

Chemistry↗
DOE OSTI2021

Low-temperature breakdown of many-body perturbation theory for thermodynamics

It is shown analytically and numerically that the finite-temperature many-body perturbation theory in the grand canonical ensemble has zero radius of convergence at zero temperature when the energy ordering or degree of degeneracy for the ground state changes with the perturbation strength. When the degeneracy of the reference state is partially or fully lifted at the first-order Hirschfelder-Certain degenerate perturbation theory, the grand potential and internal energy diverge as T → 0. Contrary to earlier suggestions of renormalizability by the chemical potential μ, this nonconvergence, first suspected by W. Kohn and J. M. Luttinger, is caused by the nonanalytic nature of the Boltzmann factor e –E/k e T at T = 0, also plaguing the canonical ensemble, which does not involve chemical potential. The finding reveals a fundamental flaw in perturbation theory, which is deeply rooted in the mathematical limitation of power-series expansions and is unlikely to be removed within its framework.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Reimagining Earth in the Earth System

Abstract Terrestrial, aquatic, and marine ecosystems regulate climate at local to global scales through exchanges of energy and matter with the atmosphere and assist with climate change mitigation through nature‐based climate solutions. Climate science is no longer a study of the physics of the atmosphere and oceans, but also the ecology of the biosphere. This is the promise of Earth system science: to transcend academic disciplines to enable study of the interacting physics, chemistry, and biology of the planet. However, long‐standing tension in protecting, restoring, and managing forest ecosystems to purposely improve climate evidences the difficulties of interdisciplinary science. For four centuries, forest management for climate betterment was argued, legislated, and ultimately dismissed, when nineteenth century atmospheric scientists narrowly defined climate science to the exclusion of ecology. Today's Earth system science, with its roots in global models of climate, unfolds in similar ways to the past. With Earth system models, geoscientists are again defining the ecology of the Earth system. Here we reframe Earth system science so that the biosphere and its ecology are equally integrated with the fluid Earth to enable Earth system prediction for planetary stewardship. Central to this is the need to overcome an intellectual heritage to the models that elevates geoscience and marginalizes ecology and local land knowledge. The call for kilometer‐scale atmospheric and ocean models, without concomitant scientific and computational investment in the land and biosphere, perpetuates the geophysical view of Earth and will not fully provide the comprehensive actionable information needed for a changing climate.

Meteorology & Atmospheric Sciences↗
DOE OSTI2021

A critical review of molybdenum sequestration mechanisms under euxinic conditions: Implications for the precision of molybdenum paleoredox proxies

The observed difference in molybdenum (Mo) mobility and isotopic fractionation under oxic versus euxinic (i.e., anoxic and sulfidic) aqueous conditions provides a sound operational basis for the use of Mo geochemical signatures in ancient sedimentary records to infer palaeoceanographic redox conditions. While Mo is known to exist predominantly as molybdate (MoO 4 2– ) in oxic waters and convert into thiomolybdate species (MoO x S 4-x 2– ) under euxinic conditions, the pathways that lead to Mo sequestration are highly debated. As mechanistic understanding of Mo sequestration is crucial for accurately reconstructing the chemistry of ancient oceans and constraining the timing and intensity of oxygenation events through Earth's history using Mo paleoproxies, we have closely examined the current proposed mechanisms for Mo sequestration across a wide range of euxinic conditions. Through compilation and comparison of such information, we aim to provide an integrated view of Mo sequestration processes, to identify the current controversies as well as the roots of such controversies, and importantly, to propose avenues for future research. Here, sequestration of Mo may occur through complexation with organic matter (OM), reactions with oxyhydroxide and sulfide mineral surfaces, incorporation into iron sulfide crystal structures, formation of Mo-sulfide, and cellular assimilation. However, several major questions remains unresolved, including whether OM complexation plays a significant role in overall sedimentary Mo accumulation, whether the reduction of Mo(VI) occurs during interaction with Fe-S clusters/precipitates and/or with OM, whether microbial enzymatic reduction of Mo(VI) is important in Mo sequestration, whether synergistic effects exist between the biological and abiotic processes in Mo sequestration, and whether differences in reactivity among the various thiomolybdate intermediate species and tetrathiomolybdate influence the Mo sequestration process. At the end of the review, the reliability of Mo paleoproxies is discussed and reevaluated.

58 GEOSCIENCES↗
DOE OSTI2024

Pyoverdine binding aptamers and label-free electrochemical detection of pseudomonads

Pyoverdines are iron-chelating siderophores employed by various pseudomonads to promote their growth in iron-limited environments, facilitating both beneficial and detrimental interactions with co-inhabiting microbes or hosts, including plants and animals. The fluorescent pseudomonads produce fluorescent pyoverdines comprised of a conserved central chromophore and a unique strain-specific peptidic side chain produced by non-ribosomal peptide synthetases. Pyoverdine Pf5 (PVD-Pf5) is produced by Pseudomonas protegens Pf-5, a species known for supporting plant growth and its involvement in plant pathogen control. To develop a means of exploring the dynamics of P. protegens activity in soil and in the rhizosphere, we selected DNA aptamers that specifically recognize PVD-Pf5 with high affinities. Two selected aptamers with only 16% identity in sequence were examined for structure and function. We found evidence that both aptamers form structures in their apo-forms and one aptamer has structural features suggesting the presence of a G-quadruplex. Although their tertiary structures are predicted to be different, both aptamers bind the target PVD-Pf5 with similar affinities and do not bind other siderophores, including the related pyoverdine, pseudobactin, produced by Pseudomonas sp. B10. One aptamer binds the pyoverdine peptide component and may also interact with the chromophore. This aptamer was integrated into a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PVD-Pf5 and not to detect other siderophores that do not bind to the aptamer when evaluated in solution. This sensor provides a future opportunity to track the locations of P. protegens around plant roots and to monitor PVD-Pf5 production and movement through the soil.

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

Crystal structure of perfluorononanoic acid, C 9 HF 17 O 2

The crystal structure of perfluorononanoic acid (PFNA) was solved via parallel tempering using synchrotron powder diffraction data obtained from the Brockhouse X-ray Diffraction and Scattering (BXDS) Wiggler Lower Energy (WLE) beamline at the Canadian Light Source. PFNA crystallizes in monoclinic space group P2 1 /c (#14) with lattice parameters a = 26.172(1) Å, b = 5.6345(2) Å, c = 10.9501(4) Å, and β = 98.752(2)°. The crystal structure is composed of dimers, with pairs of PFNA molecules connected by hydrogen bonds via the carboxylic acid functional groups. The Rietveld-refined structure was compared to a density functional theory-optimized structure, and the root-mean-square Cartesian difference was larger than normally observed for correct powder structures. The powder data likely exhibited evidence of disorder which was not successfully modeled.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Rice husk and charred husk amendments increase porewater and plant Si but water management determines grain As and Cd concentration

Abstract Purpose Rice is a staple crop worldwide and a silicon (Si) hyperaccumulator with Si levels reaching 5–10% of its mass; this can result in desilication and Si-deficiency if plant residues are not managed correctly. Rice is also uniquely subject to arsenic (As) and cadmium (Cd) contamination depending on soil conditions. Our goal is to quantify the effects of rice husk (a Si-rich milling byproduct) amendments and different water management strategies on rice uptake of Si, As, and Cd. Methods We employed 4 husk amendment treatments: Control (no husk), Husk (untreated husk), Biochar (husk pyrolyzed at 450 °C), and CharSil (husk combusted at > 1000 °C). Each of these amendments was studied under nonflooded, alternate wetting and drying (AWD), and flooded water management in a pot study. Porewater chemistry and mature plant elemental composition were measured. Results Husk and Biochar treatments, along with flooding, increased porewater and plant Si. Vegetative tissue As decreased with increasing porewater Si, but grain As and plant Cd were primarily controlled by water management. Grain As and Cd were inversely correlated and are simultaneously minimized in a redox potential (Eh) range of 225–275 mV in the studied soil. Ferrihydrite in root iron plaque decreased As translocation from porewater to grain, but amendments were not able to increase plaque ferrihydrite content. Conclusion We conclude moderate husk amendment rates (i.e., 4 years’ worth) with minimal pretreatment strongly increases rice Si content but may not be sufficient to decrease grain As in low Si and As soil.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Good, the Bad, and the Ugly: Pseudopotential Inconsistency Errors in Molecular Applications of Density Functional Theory

The pseudopotential (PP) approximation is one of the most common techniques in computational chemistry. Despite its long history, the development of custom PPs has not tracked with the explosion of different density functional approximations (DFAs). As a result, the use of PPs with exchange/correlation models for which they were not developed is widespread, although this practice is known to be theoretically unsound. The extent of PP inconsistency errors (PPIEs) associated with this practice has not been systematically explored across the types of energy differences commonly evaluated in chemical applications. Here, we evaluate PPIEs for a number of PPs and DFAs across 196 chemically relevant systems of both transition-metal and main-group elements, as represented by the W4-11, TMC34, and S22 data sets. Near the complete basis set limit, these PPs are found to cleanly approach all-electron (AE) results for noncovalent interactions but introduce root-mean-squared errors (RMSEs) upwards of 15 kcal mol –1 into predictions of covalent bond energies for a number of popular DFAs. We achieve significant improvements through the use of empirical atom- and DFA-specific PP corrections, indicating considerable systematicity of the PPIEs. The results of this work have implications for chemical modeling in both molecular contexts and for DFA design, which we discuss.

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

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗
DOE OSTI2023

Mixing in Low Reynolds Number Reacting Impinging Jets in Crossflow

Previous efforts to model uranyl fluoride formation in an impinging jet gas reactor underpredicted spatial mixing and overpredicted chemical conversion into particulates. The previous fluid dynamics model was based on the solution of the Reynolds Averaged Navier Stokes equations. After simulating fluid dynamics, aerosol dynamics were superimposed onto CFD-simulated gas reactant species concentrations. The current work explores the influence of complex unsteady flow features on the overall flow physics and chemistry for a low Reynolds number, opposed flow, impinging jet gas reactor where there is a low Reynolds number cross flow. The objective of this study was to assess the impact of model formulation on scalar mixing and transport. Here, transient flow simulations were performed using Scale Resolving Simulations. Large-Eddy Simulations with the dynamic Smagorinsky turbulence model were performed along with simulations which directly resolved the flow. Average and root-mean-square (RMS) velocities and species concentrations were computed along with modeled and resolved turbulence kinetic energy (TKE), modeled turbulence dissipation, and modeled turbulent viscosity. Lagrangian flow tracers were also used to quantify species concentrations along path lines emanating from the jet tips. Transient simulation data were compared to results from RANS simulations using the k-ω shear stress transport (SST) model and Reynolds Stress Model (RSM). Transient simulations showed spatial mixing patterns which were more consistent with experimental data and helped elucidate the process of particle formation observed in experiments.

42 ENGINEERING↗
DOE OSTI2021

Vegetation Warming Experiment: 15N Uptake Experiment Water-Extractable Soil Nutrients, Utqiagvik (Barrow), Alaska, 2018

This dataset consists of measured water-extractable carbon and nutrients measured on soils collected from warming experiment enclosures and paired control plots. Harvest types include both natural abundance and enriched soils. Vegetation warming chambers (Zero Power) were deployed on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. These chambers (Figure 1) consistently elevated air temperatures by approximately 4°C using a self-venting system described by Lewin et al (2017). Five chambers were deployed from June 17, 2018 to September 24, 2018 on the BEO within a 1 km2 area centered on 71.275N, -156.641W. Each chamber was co-located with an ambient plot where temperatures were not manipulated on patches of tundra containing the target species Arctagrostis latifolia. An intensive field campaign in late July investigated the impact of warming had on A. latifolia biomass, chemistry, and uptake of 15N labeled ammonia that was injected into the surface soils for one week. Initial measurements were taken on July 21, 2018. Harvest occurred on July 27, 2018. Water-extractable nutrients in soils were measured in July following harvests of A. latifolia plants and underlying soils. Availability of ammonia, nitrate, and phosphate throughout the growing season was measured by extracting nutrients bound to anion and cation binding resins deployed from July through September. Environmental variables (thaw depth, surface soil temperatures, surface soil moisture) were measured. Leaf traits and root traits of A. latifolia were also measured. The data package includes one *.csv data file and one *.pdf user guide. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The Low-Lying Electronic States of NO 2 : Potential Energy and Dipole Surfaces, Bound States, and Electronic Absorption Spectrum

Nitrogen dioxide, NO 2 , is a free radical composed of the two most abundant elements in Earth’s atmosphere, nitrogen and oxygen, and is relevant to atmospheric and combustion chemistry. The electronic structure of even its lowest-lying states is remarkably complex, with various conical intersections and Renner–Teller pairings, giving rise to complex and perturbed vibronic states. Here we report some analysis of the 18 molecular states of doublet spin-multiplicity formed by combining ground-state N( 4 S u ) and O( 3 P g ) atoms. In this work, three-dimensional potential energy surfaces were fit at the MRCI(Q)-F12/VTZ-F12 level, describing the lowest four ($\tilde X$, $\tilde A$, $\tilde B$, and $\tilde C$) electronic states. A properties-based diabatization procedure was applied to accommodate the intersections, producing energies in a quasidiabatic representation and yielding couplings that were also fit into surfaces. The low-lying vibrational levels on the ground $\tilde X$ state were computed and compared with experimental measurements. Compared to experiment, the lowest 125 calculated vibrational levels (up to 8500 cm –1 above the zero-point energy) have a root-mean-squared error of 16.5 cm –1 . In addition, dipole moments for each of the lowest four electronic states—and the transition dipoles between them—were also computed and fit. With the coupled energy and dipole surfaces, the electronic spectrum was calculated in absolute intensity and compared with experimental measurements. Detailed structure in the experimental spectrum was successfully reproduced, and the total integrated intensity matches experiment to an accuracy of ~1.5% with no empirical adjustments.

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

Thermodynamic analysis of hydrogel swelling in aqueous sodium chloride solutions

Here, a comprehensive thermodynamic model is presented for swelling and salt partitioning of poly (n-isopropyl acrylamide) hydrogels in aqueous sodium chloride (NaCl) solutions at 298 K. Together with a Helmholtz energy expression for network elastic energy, a modified electrolyte Nonradom Two-Liquid activity coefficient model is used to represent both the long-range electrostatic interactions and the short-range van der Waals interactions present in the gel phase. The model parameters include one network parameter per hydrogel system plus two binary parameters per interaction pair in the polymer–solvent-salt systems. With semiquantitave agreement with experimental data for both hydrogel swelling and salt partitioning up to salt saturation, the analysis suggests the ion hydration between NaCl and water is the root cause for hydrogel deswelling in aqueous NaCl solution at high NaCl concentrations, i.e., NaCl weight fraction >0.03. On the other hand, the strong repulsive interaction between NaCl and hydrogel polymer is the dominant factor for salt partitioning.

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

Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models

Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. Here, we transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.

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

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

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

Lanthanide transport in angstrom-scale MoS 2 -based two-dimensional channels

Rare earth elements (REEs), critical to modern industry, are difficult to separate and purify, given their similar physicochemical properties originating from the lanthanide contraction. Here, we systematically study the transport of lanthanide ions (Ln 3+ ) in artificially confined angstrom-scale two-dimensional channels using MoS 2 -based building blocks in an aqueous environment. The results show that the uptake and permeability of Ln 3+ assume a well-defined volcano shape peaked at Sm 3+ . This transport behavior is rooted from the tradeoff between the barrier for dehydration and the strength of interactions of lanthanide ions in the confinement channels, reminiscent of the Sabatier principle. Molecular dynamics simulations reveal that Sm 3+ , with moderate hydration free energy and intermediate affinity for channel interaction, exhibit the smallest dehydration degree, consequently resulting in the highest permeability. Our work not only highlights the distinct mass transport properties under extreme confinement but also demonstrates the potential of dialing confinement dimension and chemistry for greener REEs separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗