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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Specific Features of Nonlinear Spin Wave Localization in a Layered Ferromagnet under the Action of the Magnetic Anisotropy of Layers

A trilayer structure model has been investigated, in which uniaxial ferromagnetic layers and thin-film interfaces between them are characterized by the magnetic anisotropy. The magnetization perturbation induced in this structure is described by the nonlinear Schrödinger equation with a nonlinear potential, which simulates the interfaces between ferromagnetic layers. It is shown that, in this structure, two types of nonlinear spin waves can propagate along the layers, which are induced by the nonlinearity of the interfaces caused by their magnetic anisotropy. The frequencies of such localized stationary states of spin waves have been obtained in the explicit analytical form. The conditions for the existence of these states, depending on the characteristics of the layers and interfaces between them, have been established.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Physics-Informed Machine Learning from Observations for Clouds, Convection, and Precipitation Parameterizations and Analysis

Fusing learning from Earth observations from space and from the ground (e.g., ARM) with newly developed interpretable and generalizable physics-informed model structures to improve the parameterization of clouds and convection and advance the simulation, understanding and analysis of hydrological extreme events. This covers the prescribed foci of (2) predictive modeling using a hierarchy of models and (3) insight gleaned from complex data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Intrusive Uncertainty Quantification and Optimal Experiment Design in the Open-Source Pyomo Ecosystem

This contribution describes ParmEst and Pyomo.DoE, two pillars of the open-source Python-based Pyomo ecosystem for computational optimization with (partial differential) algebraic equation mathematical models. Specifically, ParmEst facilitates intrusive frequentist parameter estimation (PE) and uncertainty quantification (UQ) through built-in features, such as covariance matrix estimation, bootstrapping, and likelihood ratio tests. Complementary, Pyomo.DoE enables optimal experiment design by maximizing various metrics of the Fisher information matrix, such as A-optimality (trace), D-optimality (determinant), E-optimality (minimum eigenvalue), and ME-optimality (condition number). ParmEst and Pyomo.DoE can solve high-dimensional optimization problems by leveraging the model structure and exact derivative information. Finally, we will discuss future opportunities to integrate PE and UQ capabilities with optimization under uncertainty, including robust optimization with non-convex models via PyROS.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Vaterite Optical Petrography in Lake Sturgeon Otoliths

Vaterite occurring in fish otoliths exhibits plumose and spherulitic habits, the latter being like those grown from aqueous solutions. Vaterite spherulites are known to have sheaf-like texture and can be up to 100 μm in size. In thin section, the spherulites typically show uniaxial positive interference figures between cross-polarizers using a polarizing light microscope but without conoscopic or Bertrand lenses because the spherulites mimic the effect of these lenses. Plumose vaterite can show both uniaxial (+) and biaxial (+) interference figures with a small 2V, which suggests that crystal structural models for vaterite should have the plane of the carbonate group parallel to the optic axis or acute bisectrix. Finally, vaterite spherulites grown from aqueous solution exhibit similar structure and growth habits.

58 GEOSCIENCES↗
DOE OSTI2020

Are we modeling the properties of unconventional shales correctly?

Technological advancements have led to impressive growth in hydrocarbon (HC) production from unconventional shale reservoirs. However, major limiting factors in shale gas development are i) low recovery of gas in place (<20%), (ii) a rapid decline in well productivity, iii) release of contaminants, despite the use of advanced hydraulic fracturing fluids and multiple fracturing stages. This is mainly due to a lack of understanding of the nanoscale physicochemical properties of shales, especially that of kerogen, the macromolecule that is not only the source of the majority of the HC’s in shales but also holds most of the HC’s in adsorbed state. Over the last few years, a large number of studies have been published on simulating the physicochemical properties of shale utilizing molecular models of kerogen. However, the molecular models of kerogen input into these simulations are based on the kerogen “type” derived from a very limited number of shale samples. In this paper, we examine the variations that can exist in kerogen structure within a particular kerogen “type” across different shale basins and single shale basin at similar thermal maturity levels. We propose that using kerogen “type” based structural models for molecular simulations could lead to inaccurate estimation of HC reserves, HC recovery, HC production, frackability, and quantity and quality of produced water. Our study highlights the need for developing a better classification of kerogen based on its “molecular structure” instead of “type” for a more accurate prediction of physicochemical properties of shales.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2022

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived from a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Convergent close-coupling calculations of electron scattering on LiH

Cross sections for electron scattering on the ground state of LiH are calculated using the molecular convergent close-coupling method. The fixed-nuclei approximation is utilized, and calculations are performed at the mean internuclear separation of 3.06 𝑎 0 for projectile energies ranging from 0.1 to 500 eV. Here, a model-potential approach is utilized to treat the LiH molecule as a two-electron system, and good agreement is found with the literature for various properties of the structure model. Cross sections are presented for elastic scattering, excitation to several electronic states, and ionization. Comparison is made with existing results, and qualitative agreement is found with small close-coupling calculations at low projectile energies. Good agreement is found with first-order results at high projectile energies.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Geothermal Play-Fairway Analysis of Washington State Prospects: Phase 2 Technical Report

An investment of $0.7M from the Geothermal Technology Office for Phase 2 of Play Fairway Analysis in Washington State improved existing favorability models and increased model confidence. New 1:24,000-scale geological mapping, 15 detailed geophysical surveys, 2 passive seismic surveys, and geochronology collected during this phase were coupled with updated and detailed structural modeling and have significantly improved the conceptual models of three potential blind geothermal systems/ plays in Washington State, the St. Helens Shear Zone, Mount Baker, and Wind River Valley. Results of this analysis reveal the presence of commercially viable undiscovered geothermal resources in all three study areas. The analysis additionally provides a clear definition of the geothermal prospects in terms of the essential elements of a functioning geothermal system, the confidence in these assessments, and associated potential and risk of development. This report also includes a proposal to validate the modeling results in highly favorable areas for two main reasons: (1) to develop confidence in the modeling approach that will encourage future development of geothermal resources in Washington State inside and outside of the Phase 2 study areas, and (2) to provide actionable results to the DOE, existing industry partners, newly identified developers, and other renewable-energy stakeholders. The proposed validation activities aim to collect new data that will further the understanding of geothermal resource potential in Washington, as well as substantiate the favorability, confidence, and risk models developed in Phases 1 and 2.

Forson, Corina↗
DOE OSTI2026

Structural Propensities in Cs2MBiX6 (M=Na, Ag; X=Cl, Br) Bismuth Halide Double Perovskites

A previously unreported low-temperature phase transition in the bismuth halide double perovskite Cs2AgBiCl6 is reported, thereby establishing trends in the structural ground state across Cs2NaBiCl6, Cs2AgBiCl6, and Cs2AgBiBr6. Using the combined toolkit of variable-temperature synchrotron X-ray and neutron powder diffraction, Raman spectroscopy, and density-functional theory–based electronic structure modeling, we demonstrate a cubic Fm¯3m → tetragonal I4/m transition upon cooling with distinct onset temperatures. Neutron powder diffraction refinements permit the unambiguously assignment of the low-temperature phase of Cs2NaBiCl6 to I4/m, correcting prior reports of an I4/mmm ground state. Cs2AgBiCl6 is also found to transforms to a structure crystallizing in the I4/m space group at low temperatures. Temperaturedependent Raman data and density-functional theory-based modeling capture the softening and freezing of out-of-phase octahedral-tilt modes and quantify relative instabilities. Solid-state nuclear magnetic resonance spectroscopy at room temperature completes the characterization and helps underpin the subtle differences in covalency across the compounds. Trends in the phase transition temperature Ts and tilt magnitudes emerge from coupled effects of halide identity, M(I)–site bonding character, and a mismatch between interatomic distances. These results establish the structure– dynamics–bonding framework for tuning tilt-driven instabilities in halide double perovskites.

Tian, Haowen↗
DOE OSTI2013

Structure Analysis of a Precipitate Phase in an Ni-Rich High Temperature NiTiHf Shape Memory Alloy

Thermal aging of the high temperature shape memory alloy 50.3Ni-29.7Ti-20Hf (at.%) introduces a novel precipitate phase, which plays an important role in improving shape memory properties. The precipitate phase was investigated by conventional electron diffraction, high resolution scanning transmission electron microscopy (STEM) and three dimensional atom probe tomography. An unrelaxed orthorhombic atomic structural model is proposed based on these observations. This model was subsequently relaxed by ab initio calculations. As a result of the relaxation, atom shuffle displacements occur, which in turn yields improved agreement with the STEM images. The relaxed structure, which is termed the “H-phase”, has also been verified to be thermodymanically stable at 0 K.

Atom probe tomography, Ni-Ti-Hf alloy, shape memor↗
DOE OSTI2022

A method for automated modeling of plasma shape control response in tokamaks

Here, a simple method commonly used in modeling of tokamak conductor and plasma response for plasma control has been extended to allow more general modeling of tokamak PF conductor circuits. This extension combines a previously existing method for integrating plasma response and tokamak circuits with a more capable circuit modeling technique derived from the theory that underlies present-day automatic circuit simulation codes. This combined method can incorporate any combination of inductors (e.g., coils), resistors, capacitors, voltage sources, and current sources, while retaining the same model structure and ease of interpretation as the simple method. For many tokamaks, use of this extended method would not be the preferred approach, but for certain devices or for specialized models of a device, it is useful and occasionally essential. For example, the method has enabled fast and automated modeling of the complicated and daily-changing circuit topology used in the DIII-D tokamak. This automated modeling is essential to the support of controller design for the frequently changing requirements for DIII-D plasmas. It is likely to also find application in the workflows for new device designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Modeling the Potential Effects of New Tobacco Products and Policies. A Dynamic Population Model for Multiple Product Use and Harm

Background Recent declines in US cigarette smoking prevalence have coincided with increases in use of other tobacco products. Multiple product tobacco models can help assess the population health impacts associated with use of a wide range of tobacco products. Methods and Findings We present a multi-state, dynamical systems population structure model that can be used to assess the effects of tobacco product use behaviors on population health. The model incorporates transition behaviors, such as initiation, cessation, switching, and dual use, related to the use of multiple products. The model tracks product use prevalence and mortality attributable to tobacco use for the overall population and by sex and age group. The model can also be used to estimate differences in these outcomes between scenarios by varying input parameter values. We demonstrate model capabilities by projecting future cigarette smoking prevalence and smoking-attributable mortality and then simulating the effects of introduction of a hypothetical new lower-risk tobacco product under a variety of assumptions about product use. Sensitivity analyses were conducted to examine the range of population impacts that could occur due to differences in input values for product use and risk. We demonstrate that potential benefits from cigarette smokers switching to the lower-risk product can be offset over time through increased initiation of this product. Model results show that population health benefits are particularly sensitive to product risks and initiation, switching, and dual use behaviors. Conclusion Our model incorporates the variety of tobacco use behaviors and risks that occur with multiple products. As such, it can evaluate the population health impacts associated with the introduction of new tobacco products or policies that may result in product switching or dual use. Further model development will include refinement of data inputs for non-cigarette tobacco products and inclusion of health outcomes such as morbidity and disability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural Polymorphism of Chitin and Chitosan in Fungal Cell Walls From Solid-State NMR and Principal Component Analysis

Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13 C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity to the model structures of α- and γ-allomorphs; therefore, chitin structure is not significantly affected by interactions with other cell wall components. Addition of antifungal drugs and salts did not significantly perturb the chemical shifts, revealing the structural resistance of chitin to external stress. In addition, the structure of the deacetylated form, chitosan, was found to resemble a relaxed two-fold helix conformation. This study provides high-resolution information on the structure of chitin and chitosan in their cellular contexts. The method is applicable to the analysis of other complex carbohydrates and polymer composites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A Generic Biogeochemical Module for Earth System Models: Next Generation BioGeoChemical Module (NGBGC), Version 1.0

Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from atmosphere, influencing global climate changes. Integration of these processes into earth system models (e.g., community land models (CLM)), however, currently faces three major challenges: 1) extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, 2) computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and 3) various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not possible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into the CLM model. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of terrestrial ecosystems.

Fang, Yilin↗
DOE OSTI2017

Geothermal Play-Fairway Analysis of Washington State Prospects: Phase 2 Results

An investment of $0.7M from the Geothermal Technology Office for Phase 2 of Play Fairway Analysis in Washington State improved existing favorability models and increased model confidence. The new 1:24,000-scale geological mapping, 15 detailed geophysical surveys, 2 passive seismic surveys, and geochronology collected during this phase are coupled with updated and detailed structural modeling and have significantly improved the conceptual models of three potential blind geothermal systems/plays in Washington State: the St. Helens Shear Zone, Mount Baker, and Wind River Valley. Results of this analysis reveal the presence of commercially viable undiscovered geothermal resources in all three study areas. The analysis additionally provides a clear definition of the geothermal prospects in terms of the essential elements of a functioning geothermal system, the confidence in these assessments, and associated potential and risk of development. As a result, several groups have recently approached our organization about opportunities for large-capital moderate- to high-temperature geothermal development and are very interested in the results of Phase 3 drilling. Here, our updated models, coupled with development interest, provides a compelling basis for investment in future validation activities.

exploration risk↗
DOE OSTI2021

Crystal structure of the $τ_{11}$ Al 4 Fe 1.7 Si phase from neutron diffraction and ab initio calculations

The intermetallic τ 11 Al 4 Fe 1.7 Si phase is of interest for high-temperature structural application due to its combination of low density and high strength. We determine the crystal structure of the τ 11 phase through a combination of powder neutron diffraction and density functional theory calculations. Using Pawley and Rietveld refinements of the neutron diffraction data provides an initial crystal structure model. Since Al and Si have nearly identical neutron scattering lengths, we use density-functional calculations to determine their preferred site occupations. The τ 11 phase exhibits a hexagonal crystal structure with space group P6 3 /mmc and lattice parameters of a = 7.478 Å and c = 7.472 Å. The structure comprises five Wyckoff positions; Al occupies the 6h and 12k sites, Fe the 2a and 6h sites, and Si the 2a sites. Here we observe site disorder and partial occupancies on all sites with a large fraction of 80% Fe vacancies on the 2d sites, indicating an entropic stabilization of the τ 11 phase at high temperature.

36 MATERIALS SCIENCE↗