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At least 1,603 records · Page 89

A Simulation Atlas of Tidal Features in Galaxies

Detailed simulations of tidally induced structure in disk galaxies have either concentrated on specific systems or consisted of a few encounters with relatively small numbers of particles and no self-gravity. Observers need a 'dictionary' of simulations that covers many encounter parameters with fine morphological resolution and includes effects of self-gravitation. Observers can then search the dictionary for the parameters that best match a particular observed morphology. Alternatively, the dictionary can be used with observational samples for statistical studies of system parameters. To fill this need, we present a survey of model tidal encounters using a self-gravitating, 180,000 particle, two-component ('stars' and 'gas') disk. A wide variety of fascinating morphologies results. There are 86 different encounters that vary orbit tilt, perigalacticon distance, galaxy to companion mass ratio, and the amount of halo dark matter relative to the disk. For morphological comparisons, over 1700 images of the entire survey are available in video form. While there is a rich variety of tidal structure covering much of this parameter space, some general patterns may be remarked. There is a strong orbital inclination dependence of the symmetry of tidal patterns, most symmetric for planar orbits and nearly one-sided for polar encounters. Retrograde encounters produce only broad fanlike global patterns, but rich small-scale internal structure. In both kinds of encounter, our numerical resolution allows us to track internal spiral structure driven by the outer material arms, especially in the lighter halo simulations. We note also that polar encounters generate series of expanding, essentially non-rotating loops resembling shell structures in some respects.

Howard, Sethanne↗

Structural Evaluation of Exo-Skeletal Engine Fan Blades

The available computational simulation capability is used to demonstrate the structural viability of composite fan blades of innovative Exo-Skeletal Engine (ESE) developed at NASA Glenn Research Center for a subsonic mission. Full structural analysis and progressive damage evaluation of ESE composite fan blade is conducted through the NASA in-house computational simulation software system EST/BEST. The results of structural assessment indicate that longitudinal stresses acting on the blade are in compression. At a design speed of 2000 rpm, pressure and suction surface outer most ply stresses in longitudinal, transverse and shear direction are much lower than the corresponding composite ply strengths. Damage is initiated at 4870 rpm and blade fracture takes place at rotor speed of 7735 rpm. Damage volume is 51 percent. The progressive damage, buckling, stress and strength results indicate that the design at hand is very sound because of the factor of safety, damage tolerance, and buckling load of 6811 rpm.

Kuguoglu, Latife↗

Collaborative Proposal: Improving Understanding of the Internal Structure and Dynamics of Deep Convection Using ARM Observations and Large Eddy Simulations (Final progress report)

This is the final technical report for the DOE Atmospheric System Research funded project entitled "Collaborative Proposal: Improving Understanding of the Internal Structure and Dynamics of Deep Convection Using ARM Observations and Large Eddy Simulations". This project addressed several science questions related to the structure and behavior of deep convective clouds in the atmosphere. It applied knowledge gained from this work to improve the deep cumulus convection parameterization in the Community Earth System Model (CESM). Specific outcomes related to the project include an improved understanding of: (1) how convective cloud environments regulate the size of thermals reaching the upper troposphere, and hence the shallow-to-deep convective transition; (2) the role of dynamic pressure forcing in thermal and convective cloud evolution; and (3) the role of vertical wind shear on the behavior of moist thermals and the transition from shallow to deep convection. Although the primary motivation of this project was to improve basic understanding of thermal dynamics in atmospheric convection, an important component of this work was using this improved understanding to modify the representation of entrainment and vertical velocity profiles in the Zhang-McFarlane cumulus parameterization used in CESM. This work also had a strong observational component, with analyses of Atmospheric Radiation Measurement (ARM) observations to characterize thermal characteristics and behavior. Observations collected during the ARM-supported CACTI field project were used with high-resolution simulations to explore environmental controls on deep convection initiation. Data from the ARM-supported MC3E field project were also used to evaluate the representation of updraft vertical velocities in the Zhang-McFarlane cumulus parameterization. This project directly supported the training of two post-doctoral researchers and led to 16 peer-reviewed published papers.

54 ENVIRONMENTAL SCIENCES↗

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits

Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. In this report we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNa V ) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.

59 BASIC BIOLOGICAL SCIENCES↗

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

59 BASIC BIOLOGICAL SCIENCES↗

General description of nestable column structural and assembly technology

The superior packaging characteristics of nestable column structural elements make this concept attractive for application to missions space shuttle missions requiring large and/or high stiffness, or complex structures. Photographs depict investigations pursued relative to defining structural and assembly technology using these structural elements. The neutral buoyancy facility assembly simulation tests and the large space structure mobile work station are featured.

Bush, H. G.↗

Formation and Evolution of a Multi-Threaded Prominence

We investigate the process of formation and subsequent evolution of prominence plasma in a filament channel and its overlying arcade. We construct a three-dimensional time-dependent model of a filament-channel prominence suitable to be compared with observations. We combine this magnetic field structure with one-dimensional independent simulations of many flux tubes. The magnetic structure is a three-dimensional sheared double arcade, and the thermal non-equilibrium process governs the plasma evolution. We have found that the condensations in the corona can be divided into two populations: threads and blobs. Threads are massive condensations that linger in the field line dips. Blobs are ubiquitous small condensations that are produced throughout the filament and overlying arcade magnetic structure, and rapidly fall to the chromosphere. The total prominence mass is in agreement with observations. The threads are the principal contributors to the total mass, whereas the blob contribution is small. The motion of the threads is basically horizontal, while blobs move in all directions along the field. The peak velocities for both populations are comparable, but there is a weak tendency for the velocity to increase with the inclination, and the blobs with motion near vertical have the largest values of the velocity. We have generated synthetic images of the whole structure in an H proxy and in two EUV channels of the AIA instrument aboard SDO. These images show the plasma at cool, warm and hot temperatures. The theoretical differential emission measure of our system agrees very well with observations in the temperature range log T = 4.6-5.7. We conclude that the sheared-arcade magnetic structure and plasma dynamics fit well the abundant observational evidence.

Luna, M.↗

Modeling the Formation and Eruption of Coronal Structures by Linking Data-Driven Magnetofrictional and MHD Simulations for AR 12673

Context .The data-driven and time-dependent modeling of coronal magnetic fields is crucial for understanding solar eruptions. These efforts are complicated by the challenges of finding a balance between physical realism and computing efficiency. One possible technique is to couple two modeling approaches. Aims . Our aim here is to showcase our progress in using time-dependent magnetofrictional model (TMFM) results as input to dynamical magnetohydrodynamic (MHD) simulations. However, due to the different evolution processes in these two models, using TMFM snapshots in an MHD simulation is nontrivial. We address these issues, both physically and numerically, discuss the incompatibility of the TMFM output to serve as the initial condition in MHD simulations, and show our methods of mitigating this. The evolution of the flux systems and the cause of the eruption are investigated. Methods . TMFM is a prevalent approach that has proven to be a very useful tool in the study of the formation of unstable structures in the solar corona. In particular, it is capable of incorporating observational data as initial and boundary conditions and requires shorter computational time compared to MHD simulations. To leverage the efficiency of data-driven TMFM and also to simulate eruptive events in the MHD framework, one can apply TMFM up to a certain time before the expected eruption(s) and then proceed with the simulation in the full or ideal MHD regime in order to more accurately capture the eruption process. Results . We show the results of a benchmark test case with a linked TMFM and MHD simulation to study the evolution of NOAA active region 12673. A rise of a twisted flux bundle through the MHD simulation domain is observed, but we find that the rate of the rise and the altitude reached depends on the time of the TMFM snapshot that was used to initialize the MHD simulation and the helicity injected into the system. The analysis suggested that torus instability and slip-running reconnection could play an important role in the eruption. Conclusions . The results show that the linkage of TMFM and zero-β MHD models can be successfully used to model the eruptive coronal magnetic fields.

F. Daei↗

Comparison of Staggered Grid Finite Difference Schemes for Ultrasound Simulation in Curving Composites

The optimization of ultrasonic nondestructive evaluation (NDE) simulation tools for composites has the potential to reduce both individual part inspection time and overall certification time for composite parts and structures. Inspection guidance based on simulation provides increased confidence in the veracity of inspection results in addition to time reductions. This paper outlines ongoing work targeted to advance this objective through the use of finite difference (FD) simulation techniques formulated for composite structures with realistic geometries. Two staggered grid explicit FD schemes which show promise for this purpose are assessed: the Lebedev FD scheme and the rotated staggered grid (RSG) FD scheme. Algorithmic points which provide challenges for complex geometries are addressed, in particular handling of traction free surfaces and bi-material interfaces present at lamina boundaries. Code execution time estimates are performed as well to guide feasible domain sizes relative to algorithm choice and available hardware. Three test cases are simulated: a delaminated plate, a cylinder, and a triclinic lamina. These tests demonstrate that the Lebedev FD scheme needs additional work to handle inter-laminar interfaces and traction free boundaries in the presence of stair-stepping approximations. In contrast, the simple structure of the RSG unit cell makes it more straightforward to construct a 3D simulation technique for curved composite laminates.

Frankforter, Erik↗

Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study

The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a beta-(1 -> 4)/beta-(1 -> 3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (R-g) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated R-g values from the MD simulation reveal that in addition to syn-conformers the presence of anti-psi conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

Jo, Sunhwan↗

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↗

Programmable exploration of magnetic states in Lieb-kagome interpolated lattices

We investigate a hybrid modeling framework in which a quantum annealer is used to simulate magnetic interactions in molecular qubit lattices inspired by experimentally realizable systems. Using phthalocyanine assemblies as a structurally constrained prototype, we model a continuous deformation from a Lieb to a kagome lattice, revealing frustration-driven disorder and magnetic field-induced reordering in the spin structure. Here, the goal is to show how a quantum annealer can operate as a physically instantiated, programmable platform to emulate experimentally relevant lattice deformations and produce observables in a manner analogous to an experimental measurement, enabling the characterization of magnetic arrangements beyond the reach of current molecular architectures. This surrogate modeling approach offers a pathway to explore and iteratively design tunable magnetic states in synthetic materials. The synthetic design, structural characterization, and quantum simulation framework established here defines a modular and scalable paradigm for probing the limits of engineered matter across chemistry, condensed matter, and quantum information science.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Structure factors of the unitary gas under supernova conditions

Here, we compute with lattice field theory the vector and axial static structure factors of the unitary gas for arbitrary temperature above the superfluid transition and for fugacities 0.1 < $\mathcal{z}$ < 1.0 . Using the lattice formulation, we calculate beyond the validity of the virial expansion, a commonly used technique in many-body physics. We find qualitative differences in the behavior of the structure factors at high fugacity compared to the predictions of the virial expansion. Due to the large scattering length of neutrons, we expect the unitary gas structure factors to approximate the structure factors of hot neutron gases, and we therefore expect our calculations to be useful in supernova simulations, where neutron gas structure factors are needed to compute in-medium neutrino-neutron scattering rates.

79 ASTRONOMY AND ASTROPHYSICS↗

Comparison of simulated and actual wind shear radar data products

Prior to the development of the NASA experimental wind shear radar system, extensive computer simulations were conducted to determine the performance of the radar in combined weather and ground clutter environments. The simulation of the radar used analytical microburst models to determine weather returns and synthetic aperture radar (SAR) maps to determine ground clutter returns. These simulations were used to guide the development of hazard detection algorithms and to predict their performance. The structure of the radar simulation is reviewed. Actual flight data results from the Orlando and Denver tests are compared with simulated results. Areas of agreement and disagreement of actual and simulated results are shown.

Britt, Charles L.↗

Fluid Physics of Foam Evolution and Flow

The grant supported theoretical, numerical and experimental work focused on the elucidation of the fluid physics of foam structure, evolution and flow. The experimental work concentrated on these subject areas: (a) Measurements of the speed of reconnections within a foam; (b) statistics of bubble rearrangements; and (c) three-dimensional reconstruction of the foam structure. On the numerical simulation and theory side our efforts concentrated on the subjects: (a) simulation techniques for 2D and 3D foams; (b) phase transition in a compressible foam; and (c) TCP structures.

Aref, H.↗

NASA HECC Geometry and Performance Review Part 1: Validation of a Computational Model for the Vaneless Diffuser Configuration with As-Manufactured Impeller Geometry

An investigation of the NASA High Efficiency Centrifugal Compressor (HECC) vaneless diffuser configuration was performed. This multipart investigation focused on validating the computational model against experimental data. The validated model was then used to explore the effects of observed geometric differences between the as-manufactured and design-intent impellers. Lastly, the validated model was used for comparison against an experimental tip clearance study. Details regarding each of the parts are detailed below: A multipart investigation of the NASA High Efficiency Centrifugal Compressor (HECC) vaneless diffuser configuration was performed. Part I of the investigation focused on describing the HECC vaneless computational model and its validation against the experimental data published in GT2023-103128. To generate the model, a verification of the manufactured impeller was performed and was confirmed to match the impeller CAD. Section data from the impeller CAD, referred to as As-Manufactured, were used in the model. Steady RANS simulations using a multiblock structured mesh were used to conduct a mesh convergence study. The resultant mesh was then used for simulations at both design-speed and off-design speed conditions. The simulations compared well to data in both 1D and 2D terms. Based on the observed results the model was deemed validated and was used in the latter two parts of the multipart investigation.

centrifugal compressor↗

Transfer-AE: A novel autoencoder-based impact detection model for structural digital twin

Accurately detecting the location and intensity of impacts is crucial for ensuring structural safety. Currently, AI-based structural impact detection methods are widely used for their excellent detection accuracy. However, their generalization capability is limited by the scenarios present in the training data. Many complex and dangerous impact scenarios are difficult to conduct real-world experiments on to collect sufficient samples. To capture all impact scenarios and fully leverage the advantages of AI-based detection technologies, advanced methods involve combining real-world structural monitoring data with corresponding numerical models to construct digital twins. These methods continuously refine the created numerical models with limited real-world data and provide diverse impact scenarios through numerical model simulations. However, there are inevitable differences between digital models and physical models that are challenging to correct through mechanical means. This discrepancy in data distribution between the two models significantly hinders the application of digital twin technology in impact/event identification tasks. To address this challenge, this study proposes a novel model based on autoencoders, named Transfer-AE. Transfer-AE encodes the common features of digital twins in the latent space to bridge the uncertainty gap at a macro scale between numerical models and physical models and synchronously fits the magnitude and location of the impact load in the decoder. This enables consistent detection results for the same impact event, whether the sample comes from the numerical model or the physical model. Transfer-AE includes two operating modes: Mode 1 has a fixed computational complexity with stable inference speed, but the training cost and difficulty increase with data distribution. Mode 2's computational complexity increases with data distribution, but it has a fixed training cost and speed. In both cases involving the geodesic dome structure simulating a deep space habitat and the IASC-ASCE benchmark structure, Transfer-AE demonstrated the best performance in impact localization and quantification tasks compared to mainstream domain-adaptive transfer models.

Chengjia Han↗

Microphysical Variability of Amazonian Deep Convective Cores Observed by CloudSat and Simulated by a Multi-Scale Modeling Framework

Recently launched cloud observing satellites provide information about the vertical structure of deep convection and its microphysical characteristics. In this study, CloudSat reflectivity data is stratified by cloud type, and the contoured frequency by altitude diagrams reveal a doublearc structure in deep convective cores (DCCs) above 8 km. This suggests two distinct hydrometeor modes (snow versus hail/graupel) controlling variability in reflectivity profiles. The day–night contrast in the double arcs is about four times larger than the wet–dry season contrast. Using QuickBeam, the vertical reflectivity structure of DCCs is analyzed in two versions of the Superparameterized Community Atmospheric Model (SP-CAM) with single-moment (no graupel) and double-moment (with graupel) microphysics. Doublemoment microphysics shows better agreement with observed reflectivity profiles; however, neither model variant captures the double-arc structure. Ultimately, the results show that simulating realistic DCC vertical structure and its variability requires accurate representation of ice microphysics, in particular the hail/graupel modes, though this alone is insufficient.

Dodson, J. Brant↗