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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly’s global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE–p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.

Biochemistry & Molecular Biology↗
NASA NTRS1987

The climatic wind regime in the lower thermosphere from meteor radar observations

The determination of climatic norms of wind regime parameters in the lower thermosphere requires some questions of a methodical and scientific character to be settled. Among those of methodical character is: how to properly construct climatic circulation models using limited experimental data obtained by various methods during different time periods and in different geographical regions. The most important questions of a scientific character are: what main dynamic structures characterize the wind regime and how are these structures related to various atmospheric parameters and to the dynamic structures in the overlying and underlying atmospheric layers. These questions are considered and discussed.

Portnyagin, Yu. I.↗
NASA NTRS1981

The structure and dynamics of the heliospheric current sheet

It has been suggested that the sector structure observed in the interplanetary magnetic field may be interpreted in terms of a warped equatorial current sheet in the heliosphere. The reported study seeks to investigate this suggestion and to provide a clear picture of the topology of the current sheet. An analysis is presented of the magnetic field data obtained by the Pioneer 10 and 11 spacecraft during the time from 1972 to 1976, taking into account a range of heliocentric distances from 1 to 8.5 AU. The single most convincing observation in support of the warped current sheet hypothesis is the almost complete disappearance of the sector structure in the Pioneer 11 data when the spacecraft reaches a heliographic latitude of 16 deg in 1976. The observation suggests that the spacecraft was consistently above the current sheet for a period of several months.

Thomas, B. T.↗
NASA NTRS1982

Dynamics and control of a large space antenna

It is pointed out that large space antennae and other large space structures will play an important role in the coming decades as commercial applications of space become feasible. A investigation is conducted of the structural dynamics and the control properties for a 64-meter diameter center fed antenna. Attention is given to antenna configuration and structural dynamic porperties, the attitude and structural control system, disturbance assessment, hardware sizing, the construction of weighting matrices, and numerical results. It is found that structural uncertainties and model error can cause serious performance deterioration and can even destabilize the controllers. Flight test and in-orbit system identification of critical structural modes will insure performance and reduce risk for large space antenna missions.

Wang, S. J.↗
DOE OSTI2026

Effects of confinement and pressure on the structure and dynamics of carbon dioxide in silica slit pores

An understanding of carbon dioxide fluid properties within geological mesopores is important in applications ranging from carbon sequestration to shale oil recovery. Here, a molecular dynamics study is presented that aims to shed light on these systems by simulation of CO 2 fluid confined in β-cristobalite silica slit pores with different pore widths and pressure conditions. The weakly associating nature of carbon dioxide leads to little difference in structural and interfacial dynamical properties for different pore sizes and pressures. Rather, the behavior is found to be dominated by the entropic effects, namely, how the CO 2 organizes next to the silica surface. The CO 2 self-diffusion coefficient shows the strongest pore size dependence. It is strongly diminished in small pores and does not reach the bulk fluid value even in 6 nm pores. It also decreases with pressure, yielding an activation volume that increases with pore size. These results provide new insight into the behavior of a compressible fluid in nanoscale confinement.

Godahewa, Sahan M. [Univ. of Kansas, Lawrence, KS ↗
DOE OSTI2019

Structure and Dynamic and Nonlinear Optical Properties of Hg{sub 2}F{sub 2} Crystals

The structure of the Hg{sub 2}F{sub 2} compound was studied experimentally and theoretically within the density functional theory. X-ray diffraction studies enabled us to determine the space group of the crystal (I4/mmm), and the comparison of the experimentally obtained Raman spectra of these crystals with the theoretical ones enabled us to find and uniquely identify all bands in the spectra. The stability of the I4/mmm phase was analyzed in a wide range of uniaxial and hydrostatic pressures. It is shown that the uniaxial compression of a crystal along a tetrad axis results in a phase transition to the Cmcm structure at P{sub c} = 8 GPa, whereas the hydrostatic compression results in a previously unknown phase transition to the Cmca phase at P{sub c} = 9 GPa. The calculations of the cubic nonlinear susceptibility of Hg{sub 2}F{sub 2} predict a giant value of this quantity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Microscopic Structural and Dynamic Features in Triphilic Room Temperature Ionic Liquids

Here we report a thorough investigation of the microscopic and mesoscopic structural organization in a series of triphilic fluorinated room temperature ionic liquids, namely [1-alkyl,3-methylimidazolium][(trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide], with alkyl=ethyl, butyl, octyl ([C n mim][IM 14 ], n = 2, 4, 8), based on the synergic exploitation of X-ray and Neutron Scattering and Molecular Dynamics simulations. This study reveals the strong complementarity between X-ray/neutron scattering in detecting the complex segregated morphology in these systems at mesoscopic spatial scales. The use of MD simulations delivering a very good agreement with experimental data allows us to gain a robust understanding of the segregated morphology. The structural scenario is completed with determination of dynamic properties accessing the diffusive behavior and a relaxation map is provided for [C 2 mim][IM 14 ] and [C 8 mim][IM 14 ], highlighting their natures as fragile glass formers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2018

International Space Station Model Correlation Analysis

This paper summarizes the on-orbit structural dynamic data and the related modal analysis, model validation and correlation performed for the International Space Station (ISS) configuration ISS Stage ULF7, 2015 Dedicated Thruster Firing (DTF). The objective of this analysis is to validate and correlate the analytical models used to calculate the ISS internal dynamic loads and compare the 2015 DTF with previous tests. During the ISS configurations under consideration, on-orbit dynamic measurements were collected using the three main ISS instrumentation systems; Internal Wireless Instrumentation System (IWIS), External Wireless Instrumentation System (EWIS) and the Structural Dynamic Measurement System (SDMS). The measurements were recorded during several nominal on-orbit DTF tests on August 18, 2015. Experimental modal analyses were performed on the measured data to extract modal parameters including frequency, damping, and mode shape information. Correlation and comparisons between test and analytical frequencies and mode shapes were performed to assess the accuracy of the analytical models for the configurations under consideration. These mode shapes were also compared to earlier tests. Based on the frequency comparisons, the accuracy of the mathematical models is assessed and model refinement recommendations are given. In particular, results of the first fundamental mode will be discussed, nonlinear results will be shown, and accelerometer placement will be assessed.

Modal Analysis↗
DOE OSTI2026

Dynamics and Structure of Molten Neodymium Titanate

Binary rare earth titanates can be vitrified using levitation melt quenching, and their glasses are promising for optical applications. To better understand their thermophysical properties and dynamics, we have used molecular dynamics (MD) and empirical potential structure refinement (EPSR) to simulate molten neodymium titanate, 83TiO 2 –17Nd 2 O 3 . The models are compared with high-energy synchrotron X-ray diffraction of the melt structure over 1060–1960 K and thermophysical property measurements of electrostatically levitated droplets over 1500–2200 K. As temperature increases, the network periodicity increases and the correlation length decreases, both in monotonic trends that suggest continuous structural evolution through the melt and supercooled liquid regimes. At 1900 K, the mean Ti–O and Nd–O coordination numbers are 5.8(5) and 6.7(5), compared to the glass, 5.72(6) and 7.70(26). The equilibrium melting point is measured as 1860(20) K, over 100 K higher than previous estimates. Viscosity data from MD are in good agreement with experimental measurements. The dynamic propensity of Nd is similar to that of the network-forming Ti, suggesting that Nd does not participate as a conventional modifier. The viscosity of this fragile liquid is likely controlled by the breaking of cation–oxygen bonds and rearrangements of Ti–O polyhedra.

molecular dynamics↗
DOE OSTI2018

Comparison of sparse domain approaches for 4D SPECT dynamic image reconstruction

Purpose: Dynamic imaging (DI) provides additional diagnostic information in emission tomography in comparison to conventional static imaging at the cost of being computationally more challenging. Dynamic single photon emission computed tomography (SPECT) reconstruction is particularly difficult because of the limitations in the sampling geometry present in most existing scanners. We have developed an algorithm Spline Initialized Factor Analysis of Dynamic Structures (SIFADS) that is a matrix factorization method for reconstructing the dynamics of tracers in tissues and blood directly from the projections in dynamic cardiac SPECT, without first resorting to any 3D reconstruction. Methods: SIFADS is different from "pure" factor analysis in dynamic structures (FADS) in that it employs a dedicated spline-based pre-initialization. In this paper, we analyze the convergence properties of SIFADS and FADS using multiple metrics. The performances of the two approaches are evaluated for numerically simulated data and for real dynamic SPECT data from canine and human subjects. Results: For SIFADS, metrics analyzed for reconstruction algorithm convergence show better features of the metric curves vs iterations. In addition, SIAFDS provides better tissue segmentations than that from pure FADS. Measured computational times are also typically better for SIFADS implementations than those with pure FADS. Conclusion: The analysis supports the utility of the pre-initialization of a factorization algorithm for better dynamic SPECT image reconstruction.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Evolution of structure and dynamics of thermo-reversible nanoparticle gels—A combined XPCS and rheology study

A combined X-ray photon correlation spectroscopy and rheology report is carried out to capture the evolution of structure, fast particle-scale dynamics, and moduli (elastic and loss) at early times of gel formation near the fluid-gel boundary of a suspension of nanoparticles. The system is made up of moderately concentrated suspensions of octadecyl silica in decalin (φ = 0.2) undergoing thermoreversible gelation. Near the gel boundary, the rate of gel formation is very sensitive to changes in attraction strength. Yet, we find that at different attraction strengths, the system goes through identical intermediate states of microscopic and macroscopic behavior, even though the absolute time needed to form a gel varies by orders of magnitude. We identify a single dimensionless time parameter, t w /t g , where t w is the wait time following the quench and t g is the rheologically determined gel time, that captures the similarity in gel formation at a range of attraction strengths. Following a temperature quench below the gel boundary, the system is initially fluidlike and forms diffusive clusters (similar to 8.5 times the particle diameter). After a lag-time, t L , clusters aggregate to form a network like structure which is characterized by the onset of mechanical rigidity and a rapid growth in microscopic relaxation times. At t g , the Baxter parameter obtained from adhesive hard sphere fits of the structure factor attains a constant value corresponding to the theoretical percolation boundary, thus demonstrating that gelation is percolation driven.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2000

Modal Analysis and Model Correlation of the Mir Space Station

This paper will discuss on-orbit dynamic tests, modal analysis, and model refinement studies performed as part of the Mir Structural Dynamics Experiment (MiSDE). Mir is the Russian permanently manned Space Station whose construction first started in 1986. The MiSDE was sponsored by the NASA International Space Station (ISS) Phase 1 Office and was part of the Shuttle-Mir Risk Mitigation Experiment (RME). One of the main objectives for MiSDE is to demonstrate the feasibility of performing on-orbit modal testing on large space structures to extract modal parameters that will be used to correlate mathematical models. The experiment was performed over a one-year span on the Mir-alone and Mir with a Shuttle docked. A total of 45 test sessions were performed including: Shuttle and Mir thruster firings, Shuttle-Mir and Progress-Mir dockings, crew exercise and pushoffs, and ambient noise during night-to-day and day-to-night orbital transitions. Test data were recorded with a variety of existing and new instrumentation systems that included: the MiSDE Mir Auxiliary Sensor Unit (MASU), the Space Acceleration Measurement System (SAMS), the Russian Mir Structural Dynamic Measurement System (SDMS), the Mir and Shuttle Inertial Measurement Units (IMUs), and the Shuttle payload bay video cameras. Modal analysis was performed on the collected test data to extract modal parameters, i.e. frequencies, damping factors, and mode shapes. A special time-domain modal identification procedure was used on free-decay structural responses. The results from this study show that modal testing and analysis of large space structures is feasible within operational constraints. Model refinements were performed on both the Mir alone and the Shuttle-Mir mated configurations. The design sensitivity approach was used for refinement, which adjusts structural properties in order to match analytical and test modal parameters. To verify the refinement results, the analytical responses calculated using original and refined math models were compared with the measured responses. The results from this study show that the refined models predict more accurately the dynamics of the actual structure. The MiSDE test and analysis results provided the information and experience on test design, flight testing, and data analysis for the ISS and other future spacecraft, which are critical to the verification of analytical models and structural loads.

Kim, Hyoung M.↗
DOE OSTI2024

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Power Law Versus Exponential Form of Slow Crack Growth of Advanced Structural Ceramics: Dynamic Fatigue

The life prediction analysis based on an exponential crack velocity formulation was examined using a variety of experimental data on glass and advanced structural ceramics in constant stress-rate ("dynamic fatigue") and preload testing at ambient and elevated temperatures. The data fit to the strength versus In (stress rate) relation was found to be very reasonable for most of the materials. It was also found that preloading technique was equally applicable for the case of slow crack growth (SCG) parameter n > 30. The major limitation in the exponential crack velocity formulation, however, was that an inert strength of a material must be known priori to evaluate the important SCG parameter n, a significant drawback as compared to the conventional power-law crack velocity formulation.

Choi, Sung R.↗
NASA NTRS2001

Dynamic Testing of a Subscale Sunshield for the Next Generation Space Telescope (NGST)

The NGST sunshield is a lightweight, flexible structure consisting of multiple layers of pretensioned, thin-film membranes supported by deployable booms. The structural dynamic behavior of the sunshield must be well understood in order to predict its influence on observatory performance. Ground tests were carried out in a vacuum environment to characterize the structural dynamic behavior of a one-tenth scale model of the sunshield. Results from the tests will be used to validate analytical modeling techniques that can be used in conjunction with scaling laws to predict the performance of the full-sized structure. This paper summarizes the ground tests and presents representative results for the dynamic behavior of the sunshield.

Lienard, Sebastien↗
DOE OSTI2021

Real-time Characterization of the Fine Structure and Dynamics of an Electrical Double Layer at Electrode-electrolyte Interfaces

The chemisorption of species from supporting electrolytes on electrode surfaces is ubiquitous in electrochemical systems and affects the dynamics and mechanism of various electrochemical reactions. The understanding of chemical structure and property of the resulting electrical double layer is vital but limited. In this work, we operando probed the electrochemical interface between a gold electrode surface and a common supporting electrolyte, phosphate buffer, using our newly developed in situ liquid secondary ion mass spectrometry. We surprisingly found that on the positively charged gold electrode surface sodium cations were anchored in the stern layer in a partially dehydrated form by formation of compact ion pairs with the accumulated phosphate anions. The resulting strong and dense adsorption phase was further revealed to retard the electro-oxidation reaction of ascorbate. This finding addressed one major gap in the fundamental science of electrode-electrolyte interfaces that where and how the cations reside in the double layer to impose effects on electrochemical reactions, providing insights into engineering of better electrode-electrolyte interfaces in electrochemical processes.

Zhang, Yanyan↗