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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Kinetics of Shear-Induced Structural Ordering in Dense Colloids

The macroscopic rheological response of a colloidal solution is highly correlated with the local microscopic structure, as revealed by an in situ Rheo-SAXS experiment with a high temporal resolution. Oscillatory shear can induce a strain-controlled ordering-to-disorder transition, resulting in a shear-thickening process that is different from the normal shear-thickening behavior that is driven by hydrodynamics and particle friction. Here, we reveal that there is a complex time-dependent kinetics toward structural ordering under different applied strains. When the strain amplitude reaches a critical value that starts to induce disordering in the system, the pathway toward the dynamic equilibrium can also become highly non-monotonic. Within the same oscillatory cycle, there is a strong correlation of ordering with different phases of the oscillation, with the system oscillating between two dynamic metastable states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

An efficient adaptive patched grid gas dynamic solver for complex flows

The patched mesh CSCM flow solver is used with a fast adaptive grid technique to compute complex two dimensional and axisymmetric, inviscid and viscous flows accurately and efficiently. The patched grid technique allows the user to generate the initial grid around complex regions with minimal effort. The adaptive grid strategy permits the grid points to adjust to the solution in accordance with the flow structure and user specified grid constraints and thus improve the accuracy of the solution. Solutions to challenging flow problems are obtained with adapted grids and the numerical examples and the results presented here show clearly the effectiveness of the adaptive grid solution strategy to obtain highly accurate numerical solutions with minimal human effort and computational resources.

Venkatapathy, E.↗
NASA NTRS2022

VULCAN-CFD User Manual: Ver. 7.2.0

VULCAN-CFD offers a comprehensive set of capabilities to enable the simulation of continuum flowfields from subsonic to hypersonic conditions. The governing equations that are employed include allowances for both chemical and thermal nonequilibrium processes, coupled with a wide variety of turbulence models for both Reynolds-averaged and large eddy simulations. The software package can simulate two-dimensional, axisymmetric, or three-dimensional problems on structured multiblock meshes or fully unstructured meshes. A parabolic (i.e., space-marching) treatment can also be used for any subset of a structured mesh that can accommodate this solution strategy. The flow solver provides a significant level of geometric flexibility for structured grid simulations by allowing for arbitrary face-to-face C(0) continuous and non-C(0) continuous block interface connectivities. The unstructured grid paradigm allows for mixed element unstructured meshes that contain any combination of tetrahedral, prismatic, pyramidal, and hexahedral cell elements. The flow solver is also fully parallelized using MPI (Message Passing Interface) libraries in a data-parallel fashion, allowing for efficient simulations on modern High Performance Computing (HPC) systems. This document provides information related to the installation and execution of the VULCAN-CFD software package. A detailed description of the physical and numerical models available in the software are provided in the VULCAN-CFD Theory Manual.

VULCAN-CFD User Manual↗
NASA NTRS1980

On the interactions between large-scale structure and fine-grained turbulence in a free shear flow. III - A numerical solution

The results of a numerical computation of the interactions between the horizontally periodic monochromatic component of a large-scale coherent structure and the fine-grained turbulence in a mixing layer are presented. In the numerical calculations, the appropriate dependent variable is one which comprises both the mean and the large-scale coherent structure. The dynamical equations obtained for such a total coherent structure quantity are identical to the unsteady equations for the mean quantities in the Reynolds sense, except that the fine-grained turbulent stresses are interpreted as being conditionally averaged. It is shown how three dimensional fine-grained turbulence can be produced indirectly from the two dimensional large-scale structure via the isotropizing process of the approximated pressure-strain correlation.

Gatski, T. B.↗
DOE OSTI2025

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

Dynamic transformation method

Eigenvalue problem associated with modal-synthesis vibration analysis of complex structures requires simplifying assumptions for solution. Computer program, Dynamic-transformation Adapted to Modal-synthesis Using Stiffness-coupling, improves computational economy for vibration analysis of complex structures while still considering substructure modes.

Admire, J. R.↗
NASA NTRS1981

Recent developments in quasi-Newton methods for structural analysis and synthesis

Unlike the Newton-Raphson method, quasi-Newton methods by virture of the updates and step length control procedures are globally convergent and hence better suited for the solution of nonlinear problems of structural analysis and synthesis. Extension of quasi-Newton algorithms to large scale problems has led to the development of sparse update algorithms and to economical strategies for evaluating sparse Hessians. Ill-conditioning problems have led to the development of self-scaled variable metric and conjugate gradient algorithms, as well as the use of the singular perturbation theory. This paper emphasizes the effectiveness of such quasi-Newton algorithms for nonlinear structural analysis and synthesis.

Kamat, M. P.↗
NASA NTRS1987

Analysis of shell-type structures subjected to time-dependent mechanical and thermal loading

A general mathematical model and solution methodologies are being developed for analyzing structural response of thin, metallic shell-type structures under large transient, cyclic, or static thermomechanical loads. Among the system responses, which were associated with these load conditions, were thermal buckling, creep buckling, and ratcheting. Thus, geometric as well as material-type nonlinearities (of high order) can be anticipated and must be considered in the development of the mathematical model. Furthermore, this must also be accommodated in the solution process.

Simitses, G. J.↗
NASA NTRS1982

Algorithmic aspects of transient heat transfer problems in structures

It is noted that the application of finite element or finite difference techniques to the solution of transient heat transfer problems in structures often results in a stiff system of ordinary differential equations. Such systems are usually handled most efficiently by implicit integration techniques which require the solution of large and sparse systems of algebraic equations. The assembly and solution of these systems using the incomplete Cholesky conjugate gradient algorithm is examined. Several examples are used to demonstrate the advantage of the algorithm over other techniques.

Haftka, R. T.↗
NASA NTRS1992

Eigenvalue error analysis of viscously damped structures using a Ritz reduction method

The efficient solution of the eigenvalue problem that results from inserting passive dampers with variable stiffness and damping coefficients into a structure is addressed. Eigenanalysis of reduced models obtained by retaining a number of normal modes augmented with Ritz vectors corresponding to the static solutions resulting from the load patterns introduced by the dampers has been empirically shown to yield excellent approximations to the full eigenvalue problem. An analysis of this technique in the case of a single damper is presented. A priori and a posteriori error estimates are generated and tested on numerical examples. Comparison theorems with modally truncated models and a Markov parameter matching reduced-order model are derived. These theorems corroborate the heuristic that residual flexibility methods improve low-frequency approximation of the system. The analysis leads to other techniques for eigenvalue approximation. Approximate closed-form solutions are derived that include a refinement to eigenvalue derivative methods for approximation. An efficient Newton scheme is also developed. A numerical example is presented demonstrating the effectiveness of each of these methods.

Chu, Cheng-Chih↗
NASA NTRS2022

A Reinforcement Learning Hyper-Heuristic in Multi-Objective Optimization with Application to Structural Damage Identification

Multi-objective optimization allows satisfying multiple decision criteria concurrently, and generally yields multiple solutions. It has the potential to be applied to structural damage identification applications which are oftentimes under-determined. How to achieve high-quality solutions in terms of accuracy, diversity, and completeness is a challenging research subject. The solution techniques and parametric selections are believed to be problem specific. In this research, we formulate a reinforcement learning hyper-heuristic scheme to work coherently with the single-point search algorithm MOSA/R (Multi-Objective Simulated Annealing Algorithm based on Re-seed). The four low-level heuristics proposed can meet various optimization requirements adaptively and autonomously using the domination amount, crowding distance, and hypervolume calculations. The new approach exhibits improved and more robust performance than AMOSA, NSGA-II, and MOEA/D when applied to benchmark test cases. It is then applied to an active damage interrogation scheme for structural damage identification where solution diversity/completeness and accuracy are critically important. Results show that this approach can successfully include the true damage scenario in the solution set identified. The outcome of this research can potentially be extended to a variety of applications.

Pei Cao↗
NASA NTRS1999

Forced Mixer Nozzle Optimization

Computational fluid dynamic (CFD) and computational acoustic analyses (CAA) were performed for a TFE731-40 compound nozzle, a TFE731-60 mixer nozzle and an Energy Efficient Engine (E(sup 3)) mixer nozzle for comparison with available data. The CFD analyses were performed with a three dimensional, Navier-Stokes solution of the flowfield on an unstructured grid using the RAMPANT program. The CAA analyses were performed with the NASA Glenn MGB program using a structured grid. A successful aerodynamic solution for the TFE731-40 compound nozzle operating statically was obtained, simulating an engine operating on a test stand. Analysis of the CFD results of the TFE731-40 with the MGB program produced predicted sound power levels that agree quite well with the measured data front full-scale static engine tests. Comparison of the predicted sound pressure with the data show good agreement near the jet axis, but the noise levels are overpredicted at angles closer to the inlet. The predicted sound power level for the TFE731-60 did not agree as well with measured static engine data as the TFE731-40. Although a reduction in the predicted noise level due to the mixed flow was observed, the reduction was not as significant as the measured data. The analysis of the V2 mixer from the E(sup 3) study showed that peak temperatures predicted in the mixer exit flowfield were within 5 percent of the values measured by the exit probes. The noise predictions of the V2 mixer nozzle tended to be 3-5 dB higher in peak noise level than the measurements. In addition, the maximum frequency of the noise was also overpredicted. An analysis of the 3 candidate mixer nozzle configurations demonstrated the feasibility of using centerbody lobes and porosity to improve mixing efficiency. A final configuration was designed with a predicted thermal mixing efficiency that was 5 percent higher than the 3 candidate mixers. The results of the MGB noise calculations show that the final design will exceed the design goal of a 3 dB reduction in noise as compared to the baseline TFE731-40.

Sheoran, Yogi↗
NASA NTRS1988

Finite element (MARC) solution technologies for viscoplastic analyses

A need for development of realistic constitutive models for structural components operating at high temperatures, accompanied by appropriate solution technologies for stress/life analyses of these components is studied. Viscoplastic models provide a better description of inelastic behavior of materials, but their mathematical structure is very complex. The highly nonlinear and stiff nature of the constitutive equations makes analytical solutions difficult. Therefore, suitable solution, finite element or other numerical, technologies must be developed to make these models adaptable for better and rational designs of components. NASA-Lewis has developed several solution technologies and successfully applied them to the solution of a number of uniaxial and multiaxial problems. Some of these solution technologies are described along with the models and representative results. The solution technologies developed and presented encompass a wide range of models, such as, isotropic, anisotropic, metal matrix composites, and single crystal models.

Arya, V. K.↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Bifurcation analysis of a simple analytic model of self-propagating star formation

We investigate the structure and stability of rotationally symmetric nonhomogeneous time-independent solutions derived from a simple analytic model of self-propagating star formation. For this purpose we employ two methodologies: We use bifurcation theoretical methods to prove the existence of nonhomogeneous axisymmetric stationary solutions of an appropriate nonlinear evolution equation for the stellar density. We show that the nonhomogeneous solution branch bifurcates from the homogeneous one at a critical parameter value of the star formation rate. Further, the analytical theory allows us to show that the new solution set is stable in the weakly nonlinear regime near the bifurcation point. To follow the solution branch further, we use numerical methods. The numerical calculation shows the structure and stability of these solutions. We conclude that no periodic time-dependent solutions of this special model exist, and no further bifurcations can be found. The same results have been found in simulations of stochastic self-propagating star formation based on similar models. Therefore, our findings provide a natural explanation, why long-lived large-scale structure have not been found in those simulations.

Neukirch, Thomas↗
NASA NTRS2017

S-band Smallsat InSAR Constellation for Surface Deformation Science

Surface deformation studies using repeat-pass interferometric SAR have evolved into a powerful tool for geophysicists studying earthquake fault zones, volcanoes, ice sheet motion, and subterranean aquifers. Longer wavelengths (S-Band and L-Band) are preferred because they do not decorrelate as quickly as shorter wavelengths. Rapid revisit (1-3 days) is preferred because it allows the study of these phenomena at the timescales at which they commonly occur. Global access on such timescales is also required. Vector surface deformation measurements, taken from more than one direction, are a desired feature. This paper describes the conceptual architecture of a longer wave length, Smallsat SAR constellation of up to 12 satellites for rapid revisit surface deformation studies. The key to making such a constellation affordable is to lower launch costs, spacecraft costs, and instrument (SAR) costs. The first two objectives can be achieved using an ESPA-ring class, or Smallsat spacecraft. The third objective requires a SAR instrument sized to fit the mass and volume constraints imposed by such a spacecraft. Current state-of-the-art in miniaturization of electronics means that the radar transmit, receive and data handling functions can easily be implemented in a compact, low mass solution. The most significant challenge in designing a SAR to fit the Smallsat paradigm is in the dimensions of the antenna. The antenna sizing problem is addressed by adopting a smaller antenna than allowed by conventional SAR design rules. The baseline antenna design is simple, requiring no electronic beam-steering or beam-forming capability. Both reflectarray and microstrip patch antenna solutions are considered. The antenna structure is dual-purpose, to limit the overall system mass, with solar panels on the backplane providing power for the radar and spacecraft. The proposed solution easily accommodates radar squint angles of +/-30 degrees for repeat-pass interferometry measurements from multiple direct

Freeman, Anthony↗
DOE OSTI2024

Efficient real space formalism for hybrid density functionals

We present an efficient real space formalism for hybrid exchange-correlation functionals in generalized Kohn–Sham density functional theory (DFT). In particular, we develop an efficient representation for any function of the real space finite-difference Laplacian matrix by leveraging its Kronecker product structure, thereby enabling the time to solution of associated linear systems to be highly competitive with the fast Fourier transform scheme while not imposing any restrictions on the boundary conditions. We implement this formalism for both the unscreened and range-separated variants of hybrid functionals. We verify its accuracy and efficiency through comparisons with established planewave codes for isolated as well as bulk systems. In particular, we demonstrate up to an order-of-magnitude speedup in time to solution for the real space method. We also apply the framework to study the structure of liquid water using ab initio molecular dynamics, where we find good agreement with the literature. Overall, the current formalism provides an avenue for efficient real-space DFT calculations with hybrid density functionals.

Chemistry↗
DOE OSTI2025

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗