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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Machine Learned Hückel Theory: Interfacing Physics and Deep Neural Networks

The Hückel Hamiltonian is an incredibly simple tight-binding model known for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only two types of empirically fit physics-motivated parameters: the first describes the orbital energies on each atom and the second describes electronic interactions and bonding between atoms. By replacing these empirical parameters with machine-learned dynamic values, we vastly increase the accuracy of the extended Hückel model. The dynamic values are generated with a deep neural network, which is trained to reproduce orbital energies and densities derived from density functional theory. The resulting model retains interpretability, while the deep neural network parameterization is smooth and accurate and reproduces insightful features of the original empirical parameterization. Altogether, this work shows the promise of utilizing machine learning to formulate simple, accurate, and dynamically parameterized physics models.

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

Transport and confinement physics: Chapter 2 of the special issue: on the path to tokamak burning plasma operation

Progress in physics understanding and theoretical model development of plasma transport and confinement (TC) in the ITPA TC Topical Group since the publication of the ITER Physics Basis (IPB) document (Doyle et al 2007 Nucl. Fusion 47 S18) was summarized focusing on the contributions to ITER and burning plasma prediction and control. This paper provides a general and streamlined overview on the advances that were mainly led by the ITPA TC joint experiments and joint activities for the last 15 years (see JEX/JA table in appendix). This paper starts with the scientific strategy and scope of the ITPA TC Topical group and overall picture of the major progress, followed by the progress of each research field: particle transport, impurity transport, ion and electron thermal turbulent transport, momentum transport, impact of 3D magnetic fields on transport, confinement mode transitions, global confinement, and reduced transport modeling. Cross references with other Topical Groups are given in order to highlight overlapped topics, such as the 3D effect on the plasma transport in the edge and L-H transition physics. The increasing overlap between the topical groups is a reflection of the progress on integrating the known physics into comprehensive models that are better and better able to reproduce the plasma transport. In recent years, such integration has become increasingly prevalent when considering transport from the SOL, through the edge pedestal, and into the plasma core. In the near future, increased collaboration also with the magneto-hydrodynamic and energetic particles community will be important as we approach burning plasma conditions in next-step fusion devices. A summary of remaining challenges and next steps for each research field is given in the Summary section.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Narrative for Bioproject PRJNA623111

This Narrative is part of a collection used in publications focused on the microbial ecology of fjord sediment in the high Arctic, Svalbard. This paper took a genome-centric approach to uncover novel metabolic capabilities of the Acidobacteriota clade. Metagenomic data was coupled with amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes, and transcripts (available under NCBI-Genbank Bioproject PRJNA623111), and gene expression analyses of tetrathionate-amended microcosms. This Narrative contains the metagenomic assemblies that were constructed within KBase for reproducibility. These include: stnF metagenome assembly stnAB metagenome assembly stnAC metagenome assembly These metagenome assemblies served as the launching point for an additional publication focused on a different clade of bacteria (Buongiorno et al., 2020). Link to that Narrative landing page here. Please cite: Flieder, Mathias, Joy Buongiorno, Craig W. Herbold, Bela Hausmann, Thomas Rattei, Karen G. Lloyd, Alexander Loy, and Kenneth Wasmund. "Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling." The ISME Journal (2021): 1-22.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microscopic calculation of fission product yields with particle-number projection

Fission fragments' charge and mass distribution is an important input to applications ranging from basic science to energy production or nuclear nonproliferation. In simulations of nucleosynthesis or calculations of superheavy elements, these quantities must be computed from models, as they are needed in nuclei where no experimental information is available. Until now, standard techniques to estimate these distributions were not capable of accounting for fine-structure effects, such as the odd-even staggering of the charge distributions. In this work, we combine a fully microscopic collective model of fission dynamics with a recent extension of the particle number projection formalism to provide the highest-fidelity prediction of the primary fission fragment distributions for the neutron-induced fission of 235 U and 239 Pu. Here, we show that particle-number projection is an essential ingredient to reproduce odd-even staggering in the charge yields and benchmark the performance of various empirical probability laws that could simulate its effect. This new approach also enables for the first time the realistic determination of two-dimensional isotopic yields within nuclear density functional theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Time-lapse approach to correct deficiencies of 2D soil zymography

Membrane zymography is commonly used in rhizosphere ecology to map enzyme activities in intact soil samples and plant roots. The method consists of incubating a membrane saturated with an enzyme-specific fluorogenic substrate on the soil/root surface followed by measurements of fluorescence intensity of the product in the membrane. The traditional zymography is based on assumptions that fluorescence on membrane images is linearly increasing with time during zymography and an increase in product content is numerically equal to enzyme activity in soil below the membrane. These assumptions are unlikely to hold in experimental settings. In this work we introduce a new zymography technique, time-lapse zymography (TLZ); the approach that eliminates the need for assumptions of the traditional zymography and provides more realistic estimates of enzymatic activities. We assessed the new technique in a series of laboratory and modeling experiments, including quantification of the fluorescent product diffusion (e.g. MUF: 4-methylumbelliferone) from plant roots, enzyme activity measurements on the roots, and HYDRUS-2D & HP2 software calibration with obtained data. The calibrated model was used to analyze the processes governing spatial and temporal dynamics of MUF contents in the membrane. The results indicated that the enzyme diffusion within the membrane-soil system was negligible, and measured zymograms were adequately reproduced solely by accounting for substrate and product diffusions and for catalytic enzyme reaction described by the Michaelis-Menten equation. TLZ enabled identifying and using linear parts on MUF time series and accounting for MUF losses in each zymogram pixel, considerably improving the accuracy as compared to the traditional method. Results demonstrated that enzymatic activity from only a thin soil layer (~0.2 mm) is adequately represented in zymograms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Low-index mesoscopic surface reconstructions of Au surfaces using Bayesian force fields

Metal surfaces have long been known to reconstruct, significantly influencing their structural and catalytic properties. Many key mechanistic aspects of these subtle transformations remain poorly understood due to limitations of previous simulation approaches. Using active learning of Bayesian machine-learned force fields trained from ab initio calculations, we enable large-scale molecular dynamics simulations to describe the thermodynamics and time evolution of the low-index mesoscopic surface reconstructions of Au (e.g., the Au(111)-‘Herringbone,’ Au(110)-(1 × 2)-‘Missing-Row,’ and Au(100)-‘Quasi-Hexagonal’ reconstructions). This capability yields direct atomistic understanding of the dynamic emergence of these surface states from their initial facets, providing previously inaccessible information such as nucleation kinetics and a complete mechanistic interpretation of reconstruction under the effects of strain and local deviations from the original stoichiometry. We successfully reproduce previous experimental observations of reconstructions on pristine surfaces and provide quantitative predictions of the emergence of spinodal decomposition and localized reconstruction in response to strain at non-ideal stoichiometries. A unified mechanistic explanation is presented of the kinetic and thermodynamic factors driving surface reconstruction. Furthermore, we study surface reconstructions on Au nanoparticles, where characteristic (111) and (100) reconstructions spontaneously appear on a variety of high-symmetry particle morphologies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Kinetics and mechanisms of polycondensation reactions between aryl halides and bisphenol A

Aryl chlorides (ArCl) or aryl fluorides (ArF) were used in polycondensation reactions to form poly(arylene ether sulfone)s (PAES). Interestingly, the kinetics of the ArF reaction fit a third-order rate law, which is attributed to the activation of the carbon–fluorine bond by two potassium cations (at least one bound to phenolate), which form a three-body complex. Here, the ArCl monomer follows a second-order rate law, where a two-body complex forms at the initial state of the aromatic nucleophilic substitution (S N Ar) pathway. These metal cation-activated complexes act as intermediates during the attack by the nucleophile. This finding was reproduced with either the potassium or the sodium counterion (introduced via potassium carbonate or sodium carbonate). Through a combination of experimental analysis of reaction kinetics and computational calculations with density functional theory (DFT) methods, the present work extends the fundamental understanding of polycondensation mechanisms for two aryl halides and highlights the importance of the CX–metal interaction(s) in the S N Ar reaction, which is translational to other ion-activated substitution reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Applications of targeted proteomics in metabolic engineering: advances and opportunities

Optimization of metabolically engineered organisms requires good understanding of producing balanced level of pathway proteins. Targeted proteomics via selected-reaction monitoring (SRM) has been increasingly used in metabolic engineering studies to detect and quantify sets of proteins with high selectivity, multiplexity, and reproducibility. In combination with metabolomics and other omics tools, targeted proteomics has helped optimize the production of many bio-based chemicals in various metabolic engineering cell factories. In this review, we present recent applications of targeted proteomics in metabolic engineering studies and highlight several successful cases of targeted proteomics in boosting production of commodity and high value chemicals. Additionally, we also discuss challenges and limitations of current targeted proteomics and map opportunities for future research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A scalable and tunable thermoreversible polymer for 3D human pluripotent stem cell biomanufacturing

Human pluripotent stem cells (hPSCs) are an exciting and promising source to enable cell replacement therapies for a variety of unmet medical needs. Though hPSCs can be successfully derived into numerous physiologically relevant cell types, effective translation to the clinic is limited by challenges in scalable production of high-quality cells, cellular immaturity following the differentiation process, and the use of animal-derived components in culture. To address these limitations, we have developed a fully defined, reproducible, and tunable thermoreversible polymer for high-quality, scalable 3D cell production. Our reproducible synthesis method enables precise control of gelation temperature (24°C–32°C), hydrogel stiffness (100–4000 Pa), and the prevention of any unintended covalent crosslinking. After material optimization, we demonstrated hPSC expansion, pluripotency maintenance, and differentiation into numerous lineages within the hydrogel. Overall, this 3D thermoreversible hydrogel platform has broad applications in scalable, high-quality cell production to overcome the biomanufacturing burden of stem cell therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Machine learning the Hubbard U parameter in DFT+U using Bayesian optimization

Abstract Within density functional theory (DFT), adding a Hubbard U correction can mitigate some of the deficiencies of local and semi-local exchange-correlation functionals, while maintaining computational efficiency. However, the accuracy of DFT+U largely depends on the chosen Hubbard U values. We propose an approach to determining the optimal U parameters for a given material by machine learning. The Bayesian optimization (BO) algorithm is used with an objective function formulated to reproduce the band structures produced by more accurate hybrid functionals. This approach is demonstrated for transition metal oxides, europium chalcogenides, and narrow-gap semiconductors. The band structures obtained using the BO U values are in agreement with hybrid functional results. Additionally, comparison to the linear response (LR) approach to determining U demonstrates that the BO method is superior.

Chemistry↗
DOE OSTI2021

Two-dimensional turbulence in a massless fluid with a relativistic lattice Boltzmann model

We investigate a relativistic adaptation of the lattice Boltzmann method that reproduces the equations of motion for a turbulent, two-dimensional, massless hydrodynamic system. The classical lattice Boltzmann method and its extension to relativistic fluid dynamics are described. The numeric formulation is evaluated using a zero-averaged stirring force introduced into the numerics to induce turbulence, and the flow characteristics produced are compared to properties of a classical turbulent hydrodynamic flow. The model can reasonably be expected to offer quantitative simulations of electron fluid flows in graphene or Kagome lattices.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Non-Destructive In-Process Assessment of Thermal Spray Repairs

This exploratory project, entitled “Non-Destructive In-process Assessment of Thermal Spray Repairs,” evaluated the capabilities and limitations of four non-destructive testing (NDE) technologies for detection of defects in as-sprayed thermal spray coatings: acousto-ultrasonics, vibro-thermography, thermal wave infrared (IR) imaging, and flash IR thermography. The project goal was to identify a single technology suitable for use as an in-process inspection for two common classes of defects in thermal spray coatings, porosity and disbonds. Two rounds of test coupons were fabricated with intentionally seeded defects in AISI 420 stainless steel coatings deposited by twin wire arc (TWA) spray onto gray cast iron substrates. These standardized test coupons allowed the sensitivity of the four NDE methods to be directly compared. The results indicated that the acousto-ultrasonic method will not meet requirements for accuracy, inspection time, and reproducibility, while the vibrothermography method will not meet requirements for integration within remanufacturing cells and process flows. The IR methods, thermal wave imaging and flash thermography, both exhibited acceptable accuracy and reproducibility; however, the former method does not meet the requirement for inspection time. Flash IR thermography met all requirements in the initial round of testing, and that result was confirmed in a second round of testing on samples with a larger, more complex geometry. A final recommendation for further development of flash IR thermography was therefore made based upon i) detection performance, and ii) feasibility of deployment into the target application of resurfacing CAT engine blocks and headers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Evaluation of Corrosion and Its Impact on the Mechanical Performance of Al–Steel Joints

Aluminum–steel joints are increasingly used in the automotive industry to meet the requirements for energy saving and emission reduction. Among various joining technologies, self-pierce riveting (SPR) and resistance spot welding (RSW) are two well-established technologies for fabricating dissimilar joints with stable and high mechanical performance. However, corrosion will occur in these joints inevitably due to different electrochemical properties, which can degrade the surface quality and the mechanical performance, such as strength. This paper presents a method of understanding the corrosion mechanisms in joining aluminum and steel. For this understanding, a hybrid method combining experimental observations, mechanical properties identification, and analytical approaches was used to assess the evolution of the impact of corrosion on the joining performance, such as traction separation curves. The study was conducted on common combinations used in the vehicles, e.g., a 1.2 mm thickness aluminum alloy (AA 6022) and 2.0 mm thickness hot deep galvanized steel (HDG HSLA 340) joined by SPR and RSW. After the fabrication of these joints, accelerated cyclic corrosion tests of up to 104 cycles were performed, which reproduced the environmental conditions to which a vehicle was exposed. By investigating the microstructural evolution within the joints, the corrosion mechanisms of SPR and RSW joints were revealed, including the initiation and propagation. Moreover, the intrinsic impact of the corrosion on the mechanical performance, including the strength, axial stiffness, and crashworthiness, was analyzed by performing a lap-shear test. It showed that as corrosion proceeds, the fracture modes and mechanical performance are affected significantly.

Chemistry↗
DOE OSTI2023

Applications of physics informed neural operators

Abstract We present a critical analysis of physics-informed neural operators (PINOs) to solve partial differential equations (PDEs) that are ubiquitous in the study and modeling of physics phenomena using carefully curated datasets. Further, we provide a benchmarking suite which can be used to evaluate PINOs in solving such problems. We first demonstrate that our methods reproduce the accuracy and performance of other neural operators published elsewhere in the literature to learn the 1D wave equation and the 1D Burgers equation. Thereafter, we apply our PINOs to learn new types of equations, including the 2D Burgers equation in the scalar, inviscid and vector types. Finally, we show that our approach is also applicable to learn the physics of the 2D linear and nonlinear shallow water equations, which involve three coupled PDEs. We release our artificial intelligence surrogates and scientific software to produce initial data and boundary conditions to study a broad range of physically motivated scenarios. We provide the source code , an interactive website to visualize the predictions of our PINOs, and a tutorial for their use at the Data and Learning Hub for Science .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Scripts and data associated with a manuscript linking soil and sediment elemental composition with dissolved organic matter chemistry across CONUS

This data package provides scripts and geochemical data for a manuscript titled “Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry across the contiguous United States” (preprint: doi: 10.22541/essoar.169447343.31694990/v1). This data is associated with the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS, https://whondrs.pnnl.gov) and is an extension of the Summer 2019 Sampling campaign which crowdsourced samples from rivers and sediment across the continental United States. Data from this study can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775 and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719. The main objective of this manuscript was to couple sediment water extractable dissolved organic matter chemistry, defined by ultra-high resolution mass spectrometry, with localized sediment elemental composition and watershed scale soil elemental characteristics. This data package contains one main folder with four subfolders. The main data folder contains (1) readme; (2) data dictionary (dd); (3) file-level metadata (flmd); (4) an R markdown to reproduce manuscript figures and analyses; (5) a pdf of instructions to reproduce NGS interpolations with ArcGIS software; and (6) a python script to reproduce NGS extrapolations with python. The four subfolders contain files required to reproduce NGS extrapolations include (1) ‘CONUS_boundaries’ containing boundary layers (.shp) for the Continental United States; (2) ‘ngs_project’ containing files (.shp) with point level NGS soil elemental data (Grossman et al., 2004); (3) ‘raster_outputs’ containing the interpolated raster output files for various soil elements; and (4) ‘NGS_Chemistry_Final’ contain final extracted soil elemental data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum

Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

First Measurement of 87 Rb( α , xn ) Cross Sections at Weak r -process Energies in Supernova ν -driven Ejecta to Investigate Elemental Abundances in Low-metallicity Stars

Observed abundances of Z ∼ 40 elements in metal-poor stars vary from star to star, indicating that the rapid and slow neutron capture processes may not contribute alone to the synthesis of elements beyond iron. The weak r-process was proposed to produce Z ∼ 40 elements in a subset of old stars. Thought to occur in the ν-driven ejecta of a core-collapse supernova, ( α, xn ) reactions would drive the nuclear flow toward heavier masses at T = 2−5 GK. However, current comparisons between modeled and observed yields do not bring satisfactory insights into the stellar environment, mainly due to the uncertainties of the nuclear physics inputs where the dispersion in a given reaction rate often exceeds 1 order of magnitude. Involved rates are calculated with the statistical model where the choice of an α -optical-model potential ( α OMP) leads to such a poor precision. The first experiment on 87 Rb( α, xn ) reactions at weak r -process energies is reported here. Total inclusive cross sections were assessed at E c.m. = 8.1−13 MeV (3.7−7.6 GK) with the active target MUlti-Sampling Ionization Chamber. With an N = 50 seed nucleus, the measured values agree with statistical model estimates using the α OMP Atomki-V2. A reevaluated reaction rate was incorporated into new nucleosynthesis calculations, focusing on ν-driven ejecta conditions known to be sensitive to this specific rate. These conditions were found to fail to reproduce the lighter heavy element abundances in metal-poor stars.

79 ASTRONOMY AND ASTROPHYSICS↗