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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Code associated with Publication “Analytic Solutions and Field-Scale Application for Verification of Coupled Thermo-Hydro-Mechanical Processes in Subsurface Fractured Media”

As part of a submitted paper, which is collection of previously published analytical solutions to coupled thermo-hydro-mechanical problems in subsurface flow and transport, we have prepared a collection of python scripts to compute and plot those analytic solutions. All code to be released implements existing methods; there are no novel algorithms nor any major innovations to existing software.

Hyman, Jeffrey↗
DOE OSTI2025

The Measurement of Grain Size by Electron Beam Backscattered Diffraction

The method of electron back-scatter diffraction provides an analytic means to identify crystalline phase and the grain size of structural materials. The need to utilize imaging parameters consistent with revealing the contributing microstructural scale is often overlooked through packaged imaging scripts. It is shown that imaging parameters consistent with a post processing assessment of low misorientation angles between boundaries are achievable as using pixel sizes on the order of 10 1 nm.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Characterizing the Reproducibility of Noisy Quantum Circuits

The ability of a quantum computer to reproduce or replicate the results of a quantum circuit is a key concern for verifying and validating applications of quantum computing. Statistical variations in circuit outcomes that arise from ill-characterized fluctuations in device noise may lead to computational errors and irreproducible results. While device characterization offers a direct assessment of noise, an outstanding concern is how such metrics bound the reproducibility of a given quantum circuit. Here, we first directly assess the reproducibility of a noisy quantum circuit, in terms of the Hellinger distance between the computational results, and then we show that device characterization offers an analytic bound on the observed variability. We validate the method using an ensemble of single qubit test circuits, executed on a superconducting transmon processor with well-characterized readout and gate error rates. The resulting description for circuit reproducibility, in terms of a composite device parameter, is confirmed to define an upper bound on the observed Hellinger distance, across the variable test circuits. This predictive correlation between circuit outcomes and device characterization offers an efficient method for assessing the reproducibility of noisy quantum circuits.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

For your consideration: Distance Analysis for PDV Data

An analytical study that discusses photonic Doppler velocimetry data analysis methods. The author intends to share this study with experts in this field at National Laboratory partners, e.g., LLNL, LANL, and Sandia. There is no plan to submit this work to a professional (public) conference or a journal publisher.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Mind the Gap: Building Simulation in the Architectural Design Studio

Building modelling and simulation approaches are increasingly being utilized in architectural design studios to guide and inform the design process and offer evidence-based feedback on proposed building performance. The development of intuitive and simplified simulation interfaces has greatly contributed to achieving this integration. One aspect that is often overlooked is the workflow that governs and regulates integrated design, which can have significant impacts on final design outcomes. Currently there are numerous software packages available for building performance simulations. This makes it challenging to select an appropriate tool that provides accurate results yet allows a designer to make informed architectural decisions with a designer-friendly interface. Furthermore, workflows to incorporate simulations into the design process proved to highly impact student’s project design integration. Yet, it is not clear what type of workflows are successful to achieve this goal, under what conditions, and/or for which building and site typologies. This paper addresses these issues by first reviewing three different workflows for integrating building performance simulation processes and highlighting their strengths and weaknesses. Second, a comparative case study approach was employed to test three of the most common workflows in three different integrated design architectural studios at the senior and vertical studio levels as well as in two courses that run parallel and complementary to the design studios. The workflows, processes, and the resultant student projects were further analyzed based on criteria for better integrated design and architectural excellence as outlined in the American Institute of Architects Committee on the Environment (AIA COTE) Top 10 Student’s Competition. Third, to situate the pedagogical case studies’ results within a larger context, a survey of the AIA COTE Top 10 student competition award recipients over the last five years was conducted. The results are summarized in a pedagogical framework that outlines best strategies of the type of workflows, software, design process used, methods to achieve desired interaction between design process and analytical feedback, and metrics for educators to evaluate the success of this integration and their learning outcomes in the design studio. The goal is to help bridge the gap between the building design and simulation within the design studio’s creative process for more integrated design outcomes.

Elzeyadi, Ihab↗
DOE OSTI2024

Effective action approach for preheating

Abstract We present a semiclassical non-perturbative approach for calculating the preheating process at the end of inflation. Our method involves integrating out the decayed particles within the path integral framework and subsequently determining world-line instanton solutions in the effective action. This enables us to obtain the effective action of the inflaton, with its imaginary part linked to the phenomenon of particle creation driven by coherent inflaton field oscillations. Additionally, we utilize the Bogoliubov transformation to investigate the evolution of particle density within the medium after multiple inflaton oscillations. We apply our approach to various final state particles, including scalar fields, tachyonic fields, and gauge fields. The non-perturbative approach provides analytical results for preheating that are in accord with previous methods.

Astronomy & Astrophysics↗
DOE OSTI2025

Physics-guided dual implicit neural representations for source separation

Significant challenges exist in efficient data analysis of most advanced experimental and observational techniques because the collected signals often include unwanted contributions, such as background and signal distortions, that can obscure the physically relevant information of interest. To address this, we have developed a self-supervised machine-learning approach for source separation using a dual implicit neural representation framework that jointly trains two neural networks: one for approximating distortions of the physical signal of interest and the other for learning the effective background contribution. Our method learns directly from the raw data by minimizing a reconstruction-based loss function without requiring labeled data or pre-defined dictionaries. We demonstrate the effectiveness of our framework by considering a challenging case study involving large-scale simulated, as well as experimental, momentum-energy-dependent inelastic neutron scattering data in a four-dimensional parameter space, characterized by heterogeneous background contributions and unknown distortions to the target signal. The method is found to successfully separate physically meaningful signals from a complex or structured background even when the signal characteristics vary across all four dimensions of the parameter space. An analytical approach that informs the choice of the regularization parameter is presented. Our method offers a versatile framework for addressing source separation problems across diverse domains, ranging from superimposed signals in astronomical measurements to structural features in biomedical image reconstructions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Controlled expansion for pairing in a polarized band with strong repulsion

Can strong repulsive interactions be shown to give rise to pairing in a controlled way? We find that for a single flavor polarized band, there is a small expansion parameter in the low density limit, once the Bloch wavefunction form factor is taken into account. A perturbative expansion is possible, even if the interaction is much stronger than the Fermi energy ε F . As a matter of principle, our work shows analytically how strong pairing can emerge from strong repulsion. Here, we illustrate our method with two examples: a 2D Dirac model and a 1D tight binding model with two orbitals. In the latter case, using density matrix renormalization group, we show that the analytical theory indeed guided us to discover the parameter regime where p-wave pairing with order-1 strength is dominant.

Ferromagnetic superconductors↗
DOE OSTI2022

General, Rigorous Approach for the Treatment of Interfragment Covalent Bonds

Here, a generalized, projection-based transformation of the method-agnostic Fock operator in various ab initio fragment-based quantum chemistry methods has been developed for the treatment of interfragment covalent bonds. This transformation freezes the relevant localized molecular orbital associated with each interfragment bond, thereby restricting the variational subspace of the fragment wave functions, in order to maintain the proper physical characteristics of the involved covalent bonds. In addition, sets of orbitals that would lead to multiple occupancy of certain orbitals are explicitly removed from the variational space. The transformation is developed for the specific case of mutually orthonormal frozen and unfrozen orbitals within each fragment. The newly developed approach is then used to study model systems with two popular ab initio fragment-based methods, and the results of these calculations are compared to those obtained by existing methodologies. Analysis is focused on both quantitative and qualitative accuracy as well as computational scalability and stability. Other methods for which the developed formalisms are appropriate are outlined, and future extensions of the methods are discussed.

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

Unbiased particle conformation extraction from scattering spectra using orthonormal basis expansions

A strategy is outlined for quantitatively evaluating the particle density profiles from small-angle scattering spectra of dilute solutions. The approach employs an orthonormal basis function expansion method, enabling the determination of characteristic mass distributions in self-assembled structures without the need for a specific structural model. Through computational benchmarking, the efficacy of this approach is validated by effectively reconstructing the density profile of soft-ball systems with varying fuzziness from their scattering signatures. Further, the feasibility of the method is demonstrated by fitting small-angle neutron scattering data obtained from Pluronic L64 micelles at different temperatures. This proposed approach is both simple and analytical, eliminating the requirement for a presumptive structural model in scattering analysis. The new method could therefore facilitate quantitative descriptions of complex nanoscopic structures inherent to numerous soft-matter systems using small-angle scattering techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Comparison of heavy-ion transport simulations: Mean-field dynamics in a box

Within the transport model evaluation project (TMEP) of simulations for heavy-ion collisions, the mean-field response is examined here. Specifically, zero-sound propagation is considered for neutron-proton symmetric matter enclosed in a periodic box, at zero temperature and around normal density. The results of several transport codes belonging to two families (BUU-like and QMD-like) are compared among each other and to exact calculations. For BUU-like codes, employing the test particle method, the results depend on the combination of the number of test particles and the spread of the profile functions that weight integration over space. These parameters can be properly adapted to give a good reproduction of the analytical zero-sound features. QMD-like codes, using molecular dynamics methods, are characterized by large damping effects, attributable to the fluctuations inherent in their phase-space representation. Moreover, for a given nuclear effective interaction, they generally lead to slower density oscillations, as compared to BUU-like codes. The latter problem is mitigated in the more recent lattice formulation of some of the QMD codes. Furthermore, the significance of these results for the description of real heavy-ion collisions is discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

High-precision chemical quantum sensing in flowing monodisperse microdroplets

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence. Using this method, paramagnetic ions in droplets are detected with low limit-of-detection using small analyte volumes, with exceptional measurement stability over >10 3 s. In addition, these droplets are used as microconfinement chambers by co-encapsulating ND quantum sensors with various analytes such as single cells, suggesting wide-ranging applications including single-cell metabolomics and real-time intracellular measurements from bioreactors. Important advances are enabled by this work, including portable chemical testing devices, amplification-free chemical assays, and chemical imaging tools for probing reactions within microenvironments.

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

A Characteristics Approach to the Finite Element Method

Herein, we present a new method for solving the linear Boltzmann transport equation. Two commonly used and well-understood methods for solving partial differential equations are the method of characteristics (MOC) and the finite element method (FEM). We propose a new method that combines the fundamental concept of the FEM with the analytic solution from the MOC to obtain coefficients for the FEM basis function expansion. Traditionally, coefficients for the FEM basis function expansion are obtained via matrix inversion. Instead, we solve for the coefficients with the MOC and represent the underlying fields with the basis function expansion using these coefficients. We provide a convergence study for our method with results from two sets of FEM basis functions: Gauss-Legendre and Gauss-Lobatto sets. We also compare two different variations of our method categorized as short characteristics and intermediate characteristics.

42 ENGINEERING↗
DOE OSTI2022

Accurate hydrodynamic force and torque correlations for prolate spheroids from Stokes regime to high Reynolds numbers

Detailed simulations of flow around various prolate spheroids are performed using multi-relaxation time lattice Boltzmann method (LBM). The simulations are performed in the Reynolds numbers range 0.1 ≤ Re ≤ 2000 at different incident angles 0°≤ φ ≤ 90° for various prolate spheroids of aspect ratios 1 ≤ λ ≤ 8. The Re is based on the volume equivalent sphere diameter. From the simulations, accurate correlations for average drag, lift and torque coefficients (C D , C L , and C T respectively) are proposed. The mean deviations between the correlations and the simulation data for C D , C L , and C T are 2%, 6.5%, and 4.7% respectively. Furthermore, the correlations are fitted with the physics in mind such that they can be extrapolated beyond the regimes simulated. The fits are designed such that correlations reduce to analytical (C D and C L ) solutions available for prolate spheroids in the limit Re ≈ 0. At high Re, the correlations mimic the asymptotic flattening of C D as for spheres and therefore, we expect the correlations to be valid until the critical Re (≈ 10 5 ). Furthermore, extensive comparison of our correlations with other high-fidelity simulations from literature demonstrate the accuracy of our work compared to other correlations from literature. This work enables researchers to perform accurate unresolved Euler-Lagrangian simulations for a wide range of elongated particles.

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

Consistent solutions of the radiation diffusion equation in spherical and cylindrical geometries

We have extended the radiation diffusion model of Hammer and Rosen [Phys. Plasmas 10, 1829 (2003)] to diverging spherical and cylindrical geometries. The effect of curvilinear geometry on the supersonic, expanding wavefront increases as the internal radius of a spherical or cylindrical shell approaches zero. Small spherical geometries are important for modeling systems at the size scale of inertial confinement fusion capsules, at these scales existing quasi-analytic models for planar geometry significantly disagree with the results of simulation. With this method, the benefits of rapid iteration can be applied to common spherical systems at much smaller length scales. We present comparisons between numerical diffusion solutions and the analytic model to give ranges of applicability for the model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Analytical derivatives of the individual state energies in ensemble density functional theory. II. Implementation on graphical processing units (GPUs)

Conical intersections control excited state reactivity, and thus, elucidating and predicting their geometric and energetic characteristics are crucial for understanding photochemistry. Locating these intersections requires accurate and efficient electronic structure methods. Unfortunately, the most accurate methods (e.g., multireference perturbation theories such as XMS-CASPT2) are computationally challenging for large molecules. The state-interaction state-averaged restricted ensemble referenced Kohn–Sham (SI-SA-REKS) method is a computationally efficient alternative. The application of SI-SA-REKS to photochemistry was previously hampered by a lack of analytical nuclear gradients and nonadiabatic coupling matrix elements. We have recently derived analytical energy derivatives for the SI-SA-REKS method and implemented the method effectively on graphical processing units. We demonstrate that our implementation gives the correct conical intersection topography and energetics for several examples. Furthermore, our implementation of SI-SA-REKS is computationally efficient, with observed sub-quadratic scaling as a function of molecular size. This demonstrates the promise of SI-SA-REKS for excited state dynamics of large molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗