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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 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Data publication with the structural biology data grid supports live analysis

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Direct numerical simulations of turbulent premixed cool flames: Global and local flame dynamics analysis

The cool flame dynamics, especially in turbulent flows, is of great interest for both practical application and fundamental research. Here, in this study, a series of direct numerical simulations of turbulent premixed n-C 7 H 16 /O 2 /O 3 /N 2 cool flames are performed, with the focus on the influence of turbulence intensity (u'/S L , where S L is the laminar flame speed) on the flame structure as well as the global and local cool flame dynamics. It is found that the cool flame front is considerably wrinkled by turbulence at high u'/S L , leading to significantly thickened turbulent cool flame brush and largely altered local reactivity compared with the reference laminar flame. However, the turbulent flame structure in the temperature space is found to be insensitive to u'/S L . Besides, with increasing u'/S L , the normalized turbulent cool flame speed (S L /S L ) is monotonically increased, attributed to substantial augmentation on the flame surface area (A T /A L ), while the stretching factor (I 0 ) remains almost constant and is smaller than 1. The underlying mechanisms for such variations are revealed through local flame dynamics analysis. Specifically, the local flame displacement speed S d is found to be strongly negatively correlated with flame curvature; meanwhile, such negative correlation and the probability distribution function (PDF) of flame curvature are barely influenced by u'/S L , leading to a weak dependence of I 0 on u'/S L . In contrast, the PDF of the tangential strain rate is found to span a much wider range and shift to the positive side as u'/S L increases, suggesting that the enhanced tangential strain rate is the main cause for the increase in surface area of the turbulent premixed cool flame. Finally, the influence of equivalence ratio on above findings is found to be insignificant, indicating that although the local reactivity of turbulent premixed cool flames is altered due to the differential diffusion, the resultant flame- stretch interaction is insensitive to the equivalence ratio. This study presents some unique cool flame dynamics that are distinct from hot flames, which can help improve the understanding and modeling of turbulent cool flames.

Cool flames↗
DOE OSTI2017

Air Flow Modeling in the Wind Tunnel of the FHWA Aerodynamics Laboratory at Turner-Fairbank Highway Research Center

Computational fluid dynamics (CFD) modeling is widely used in industry for design and in the research community to support, compliment, and extend the scope of experimental studies. Analysis of transportation infrastructure using high performance cluster computing with CFD and structural mechanics software is done at the Transportation Research and Analysis Computing Center (TRACC) at Argonne National Laboratory. These resources, available at TRACC, were used to perform advanced three-dimensional computational simulations of the wind tunnel laboratory at the Turner-Fairbank Highway Research Center (TFHRC). The goals were to verify the CFD model of the laboratory wind tunnel and then to use versions of the model to provide the capability to (1) perform larger parametric series of tests than can be easily done in the laboratory with available budget and time, (2) to extend testing to wind speeds that cannot be achieved in the laboratory, and (3) to run types of tests that are very difficult or impossible to run in the laboratory. Modern CFD software has many physics models and domain meshing options. Models, including the choice of turbulence and other physics models and settings, the computational mesh, and the solver settings, need to be validated against measurements to verify that the results are sufficiently accurate for use in engineering applications. The wind tunnel model was built and tested, by comparing to experimental measurements, to provide a valuable tool to perform these types of studies in the future as a complement and extension to TFHRC’s experimental capabilities. Wind tunnel testing at TFHRC is conducted in a subsonic open-jet wind tunnel with a 1.83 m (6 foot) by 1.83 m (6 foot) cross section. A three component dual force-balance system is used to measure forces acting on tested models, and a three degree of freedom suspension system is used for dynamic response tests. Pictures of the room are shown in Figure 1-1 to Figure 1-4. A detailed CAD geometry and CFD model of the wind tunnel laboratory at TFHRC was built and tested. Results were compared against experimental wind velocity measurements at a large number of locations around the room. This testing included an assessment of the air flow uniformity provided by the tunnel to the test zone and assessment of room geometry effects, such as influence of the proximity the room walls, the non-symmetrical position of the tunnel in the room, and the influence of the room setup on the air flow in the room. This information is useful both for simplifying the computational model and in deciding whether or not moving, or removing, some of the furniture or other movable objects in the room will change the flow in the test zone.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Semi-Annual Report for Horizontal Compact High Temperature Gas Reactor (HC-HTGR) Development during Performance Period April 2023 – September 2023

Horizontal Compact High Temperature Gas Reactor (HC-HTGR) is being designed by a multi-disciplinary team of nuclear, mechanical, and structural engineers under the support of a DOE-NE Advanced Reactor Demonstration Program’s Advanced Reactor Concepts-20 (ARC-20) award. The objective of this ARC-20 project is to deliver a conceptual design for the proposed HC-HTGR in 3 years and support its commercialization as a safe, low-cost HTGR. Argonne National Laboratory (Argonne) is responsible for the design and analysis of the reactor cavity cooling system (RCCS) as a safety system for passive decay heat removal of the reactor concept. Additionally, Argonne is providing analysis of the primary coolant system to ensure temperatures within the core remain below safety margins during steady-state and potential accident scenarios. This fourth semi-annual report summarized the progress made at Argonne on the two tasks during the second half of FY23. As a part of the RCCS design task, recent efforts have been made to complete a conceptual design of the RCCS for the HC-HTGR, including the design update of the water panel and system configuration favorable in point of view of fabrication and system operation. Design calculations were conducted under various heat load conditions to validate the system design. Transient simulations using RELAP5-3D were conducted to investigate system dynamics under transients of interest and to evaluate the system performance in the design condition. The results demonstrated the overall system feasibility that the RCCS design maintains structures temperatures lower than maximum allowable temperature with sufficient system inventory without any active heat sink. In the primary system thermal hydraulics task, the preliminary analysis was performed for a long term pressurized conduction cooldown (PCC) transient. This analysis used a combination of a fully resolved and coarse homogenized mesh to predict the temperature distribution for the steady-state initial condition and the PCC transient. The steady-state initial condition was determined using a fully resolved full core model with 3D solid to 1D fluid coupling. The fully resolved mesh was also used to model the first 20 seconds of the PCC. The temperature difference between fuel pins and the graphite matrix becomes minimal and the dominant heat transfer shifts to a larger scale radially towards the RCCS. After 20 seconds, a homogenized coarse mesh is used, greatly reducing the computational costs of the model. These results demonstrate that the core is designed to passively remove enough decay heat in a protected loss of primary coolant flow to prevent an unsafe rise of core temperatures.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment

Abstract Background Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope ( 13 C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis. Results Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13 C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13 C– 13 C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides. Conclusions By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.

09 BIOMASS FUELS↗
DOE OSTI2014

Comparing linear and cyclic synthetic homopolypeptides: Synthesis and molecular characterization

We report the synthesis and molecular characterization of a linear and a cyclic homopolypeptide of protected l-tyrosine. The successful synthesis of polypeptides exhibiting the desired linear and cyclic structures through various characterization methods such as high temperature gel permeation chromatography, Fourier transform infrared spectroscopy, proton and carbon nuclear magnetic resonance spectroscopy, mass spectrometry, dynamic light scattering, differential scanning calorimetry, and thermogravimetric analysis was verified in this work. Our results are very promising especially if such cyclic materials will be potentially used as carriers for drug delivery, either through conjugation with specific ligands or directly through the functional hydroxyl groups of the monomeric units of poly(l-Tyr) after deprotection.

36 MATERIALS SCIENCE↗
DOE OSTI2017

All-Atom Molecular Dynamics Study of Water–Dodecane Interface in the Presence of Octanol

In this work, classical atomistic molecular dynamics (MD) simulations were performed to investigate the structural properties of octanol at water/dodecane interface. Multiple combinations of simulation conditions and force fields were employed in order to :obtain high fidelity interfacial structure. The analysis of noncovalent interactions shows that the convergence of interfacial octanol distribution requires a simulation time scale larger than 100 ns. Finite size effect diminishes with increasing dimension of simulation box both laterally and vertically. In the largest simulated systems with vanishing finite size effect, the additive CHARMM force field shows similar interfacial aggregation behavior with the DRUDE polarizable model. Self-assembly of octanol molecules at water/oil interface is observed, expected to reduce;the free energy barrier between water phase and oil phase. This work provides an MD simulation benchmark for structural study of complex liquid/liquid interface with cosurfactant reducing interfacial tension between two immiscible phases.

Qiao, Baofu↗
DOE OSTI2014

Opacity and gradients in aluminum wire array z-pinch implosions on the Z pulsed power facility

Aluminum wire array z pinches imploded on the Z generator are an extremely bright source of 1–2 keV radiation, with close to 400 kJ radiated at photon energies >1 keV and more than 50 kJ radiated in a single line (Al Ly-α). Opacity plays a critical role in the dynamics and K-shell radiation efficiency of these pinches. Where significant structure is present in the stagnated pinch this acts to reduce the effective opacity of the system as demonstrated by direct analysis of spectra. Analysis of time-integrated broadband spectra (0.8–25 keV) indicates electron temperatures ranging from a few 100 eV to a few keV are present, indicative of substantial temperature gradients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Reconstruction of effective potential from statistical analysis of dynamic trajectories

The broad incorporation of microscopic methods is yielding a wealth of information on the atomic and mesoscale dynamics of individual atoms, molecules, and particles on surfaces and in open volumes. Analysis of such data necessitates statistical frameworks to convert observed dynamic behaviors to effective properties of materials. Here, we develop a method for the stochastic reconstruction of effective local potentials solely from observed structural data collected from molecular dynamics simulations (i.e., data analogous to those obtained via atomically resolved microscopies). Using the silicon vacancy defect in graphene as a model, we apply the statistical framework presented herein to reconstruct the free energy landscape from the calculated atomic displacements. Evidence of consistency between the reconstructed local potential and the trajectory data from which it was produced is presented, along with a quantitative assessment of the uncertainty in the inferred parameters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Manipulating meso-scale solvent structure from Pd nanoparticle deposits in deep eutectic solvents

Deep Eutectic Solvents (DESs) are complex solutions that present unique challenges compared to traditional electrolytes. Unlike most electrolytes and ionic liquids, DESs have delicate hydrogen bond networks that are responsible for their highly sensitive compositional dependence on the melting point. Prior work has demonstrated unique nanoscale structure both experimentally and theoretically that brings both challenges and opportunities to their adoption in traditional electrochemical processes. In this study, we use in-situ sample-rotated ultra-small angle X-ray scattering to resolve the near-interface solvent structure after electrodepositing Pd nanoparticles onto a glassy carbon electrode in choline chloride:urea and choline chloride:ethylene glycol DESs. Our results indicate that solvent structure can be observed on the meso-scale in the choline chloride:urea and choline chloride:ethylene glycol systems. Importantly, this extended solvent structure peaks at -0.5 V (vs. Ag/AgCl) and decreases slightly with higher overpotentials during Pd electrodeposition. Experimentally, the nature of this structure is more pronounced in the ethylene glycol system, as evidenced by both the X-ray scattering as well as the electrochemical impedance spectroscopy (EIS). Here, molecular dynamics simulations and dipolar orientation analysis reveal that chloride delocalization near the Pd interface and long-range interactions between the choline and each hydrogen bond donor are very different and qualitatively consistent with the experimental data. These results show how the long-range solvent-deposit interactions can be tuned by changing the hydrogen bond donor in the DES and the applied potential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na + and K + Ions and the Protonation State of Glu 290

Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In other microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K + ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na + . In this work, we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K+ binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na + ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na + in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu 290 , either charged or neutral, point to the Glu 290 protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a “water gate” opens through coordinated motions of residues Leu 25 , Tyr 108 , and Phe 253 . The resulting water channel allows the binding/dissociation of the Na + and K + ions that are prevalent, respectively, in the extracellular and intracellular environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

OBSERVING CASCADES OF SOLAR BULLETS AT HIGH RESOLUTION. II

High resolution observations from the Swedish 1-m Solar Telescope revealed bright, discrete, blob-like structures (which we refer to as solar bullets) in the Hα 656.28 nm line core that appear to propagate laterally across the solar atmosphere as clusters in active regions (ARs). These small-scale structures appear to be field aligned and many bullets become triggered simultaneously and traverse collectively as a cluster. Here, we conduct a follow-up study on these rapidly evolving structures with coincident observations from the Solar Dynamics Observatory/Atmospheric Imaging Assembly. With the co-aligned data sets, we reveal (a) an evolving multithermal structure in the bullet cluster ranging from chromospheric to at least transition region temperatures, (b) evidence for cascade-like behavior and corresponding bidirectional motions in bullets within the cluster, which indicate that there is a common source of the initial instability leading to bullet formation, and (c) a direct relationship between co-incident bullet velocities observed in Hα and He ii 30.4 nm and an inverse relationship with respect to bullet intensity in these channels. We find evidence supporting that bullets are typically composed of a cooler, higher density core detectable in Hα with a less dense, hotter, and fainter co-moving outer sheath. Bullets unequivocally demonstrate the finely structured nature of the AR corona. We have no clear evidence for bullets being associated with locally heated (or cooled), fast flowing plasma. Fast MHD pulses (such as solitons) could best describe the dynamic properties of bullets whereas the presence of a multithermal structure is new.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Quantification of spatial and seasonal trends in the atmosphere and construction of statistical models for infrasonic propagation

SUMMARY Infrasonic waves are influenced by variations in the density, pressure and temperature as well as the ambient winds. Modelling infrasonic propagation can be challenging due to the dynamic nature of the atmosphere as well as the sparseness of measurements which result in variability and notable uncertainty. A framework is presented to quantify spatial and seasonal trends in atmospheric structure via analysis of the effective sound speed profile and identification of temporal trends in the middle atmospheric waveguide produced by the circumpolar vortex winds. Seasonal definitions identifying typical atmospheric structures during the summer, winter and spring/fall transition periods are identified using atmospheric data from 2010 through 2020. Seasonal trend analysis is conducted for a number of locations across the contiguous United States to quantify spatial variations in atmospheric structure that impact infrasonic propagation. For each season and location, empirical orthogonal function analysis is used to reduce the historical archive of atmospheric data into a smaller representative set that can be analysed using numerical tools more efficiently. Infrasonic ray tracing and finite-frequency modal propagation analyses are applied to construct propagation path geometry and transmission loss statistics which are useful in localization and yield estimation for infrasonic sources, respectively. An example application is detailed in which transmission loss statistics are combined with an explosive source model and noise statistics to quantify the capability of a network to detect nearby sources.

58 GEOSCIENCES↗
DOE OSTI2017

Analysis of the Effect of Different Initial States and Structural Defects on the Characteristics of the Nonequilibrium Critical Behavior of the 3D Ising Model

The effect of different initial values m{sub 0} of magnetization and structural defects on the nonequilibrium critical behavior of the 3D Ising model have been analyzed numerically using the Monte Carlo method. Analysis of the two-time dependences of the autocorrelation function and dynamic susceptibility has revealed a substantial influence of the initial states on the aging effects that are characterized by anomalous retardation of relaxation and correlation in the system upon an increase in the waiting time. We have studied the violations of the fluctuation–dissipation theorem and calculated the limiting fluctuation–dissipation ratio. It is shown that in the nonequilibrium critical behavior of the 3D Ising model, two universality subclasses corresponding to the evolution of the system from the high-temperature (with m{sub 0} = 0) and low-temperature (with m{sub 0} = 1) initial states with the values of the limiting fluctuation–dissipation ratio typical of these states can be singled out.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Study of light nuclei by polarization observables in electron scattering

Electron-induced proton, neutron and deuteron knock-out remains the most versatile probe of the electro-magnetic properties and spin structure of light nuclei. The advent of highly polarized beams and targets and improvements in recoil polarization methods, as well as analysis and simulation techniques, have enabled us to study the static and dynamical properties of few-body systems with unprecedented precision. Recent experiments at Jefferson Lab and MAMI are presented and put into perspective of state-of-the art Faddeev calculations, with focus on the ^\mathbf{3}\mathbf{He} 3 𝐇 𝐞 nucleus.

Sirca, Simon↗
DOE OSTI2019

Lessons from a large-scale systems dynamics modeling project: the example of the biomass scenario model

The biomass scenario model (BSM) is a dynamic model of the biomass-to-biofuels supply chain in the U.S.A., developed during a multi-year analysis effort conducted by the National Renewable Energy Laboratory (NREL), under sponsorship from the United States Department of Energy (DOE) Bioenergy Technologies Office (BETO). The BSM project, which received the 2018 Applications Award by the International System Dynamics Society, has supported collaborative analyses, developed scenarios for industry development and facilitated stakeholder engagement. We summarize insights gained from the BSM project that may be useful to other large-scale dynamic modeling efforts. We summarize the project focus, the analysis process, key outcomes and observations on successful execution of such a product. Key points include the value of a multidisciplinary team with clear roles, engagement of experts and stakeholders, and use and reuse of simple, modular structures. As a result, the overall effort suggests that these practices may aid long-term, team-focused, multi-stakeholder modeling efforts.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2014

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗