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Results for “conformal maps”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

Background: Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen. Methods: Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Results: Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions. Conclusion: Further, this work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mapping the catalytic conformations of an assembly-line polyketide synthase module

Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Additionally, using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in structurally characterizing regions of high flexibility. These technical barriers have impeded characterization of flexible ribosomal proteins when the ribosome is interacting with mRNA stem-loop structures such as a frameshifting stimulatory sequence (FSS). Small-angle neutron/X-ray scattering and electron microscopy were used to study ribosomal samples and compared structural differences between a ribosome that is bound to an FSS stem-loop compared to a ribosome bound to linear mRNA. This comparison shows that a large protein stalk elongates by 22% when the 70S interacts with an mRNA stem-loop. Finally, our results suggest that ribosomal proteins have extensive flexibility and may influence important ribosomal mechanisms, such as those that involve FSS.

36 MATERIALS SCIENCE↗
NASA NTRS1979

Logarithmic spiral grids for image processing

A picture digitization grid based on logarithmic spirals rather than Cartesian coordinates is presented. Expressing this curvilinear grid as a conformal exponential mapping reveals useful image processing properties. The mapping induces a computational simplification that suggests parallel architectures in which most geometric transformations are effected by data shifting in memory rather than arithmetic on coordinates. These include fast, parallel noise-free rotation, scaling, and some projective transformations of pixel defined images. Conformality of the mapping preserves local picture-processing operations such as edge detection.

Weiman, C. F. R.↗
DOE OSTI2023

Energy landscapes from cryo-EM snapshots: a benchmarking study

Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

The performance evaluation of a new neural network based traffic management scheme for a satellite communication network

A neural-network-based traffic management scheme for a satellite communication network is described. The scheme consists of two levels of management. The front end of the scheme is a derivation of Kohonen's self-organization model to configure maps for the satellite communication network dynamically. The model consists of three stages. The first stage is the pattern recognition task, in which an exemplar map that best meets the current network requirements is selected. The second stage is the analysis of the discrepancy between the chosen exemplar map and the state of the network, and the adaptive modification of the chosen exemplar map to conform closely to the network requirement (input data pattern) by means of Kohonen's self-organization. On the basis of certain performance criteria, whether a new map is generated to replace the original chosen map is decided in the third stage. A state-dependent routing algorithm, which arranges the incoming call to some proper path, is used to make the network more efficient and to lower the call block rate. Simulation results demonstrate that the scheme, which combines self-organization and the state-dependent routing mechanism, provides better performance in terms of call block rate than schemes that only have either the self-organization mechanism or the routing mechanism.

Ansari, Nirwan↗
DOE OSTI2024

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism

Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental access. This shortcoming is evident with Escherichia coli dihydrofolate reductase (DHFR), a model system for the role of protein dynamics in catalysis, for which it is unknown how the enzyme regulates the different active site environments required to facilitate proton and hydride transfer. Here, we describe ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments to map the conformational dynamics of the Michaelis complex of DHFR. We resolve coupled global and local motions and find that these motions are engaged by the protonated substrate to promote efficient catalysis. This result suggests a fundamental design principle for multistep enzymes in which pre-existing dynamics enable intermediates to drive rapid electrostatic reorganization to facilitate subsequent chemical steps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Theoretical Assessment of the Transition Between Electron Emission Mechanisms for Nonplanar Diodes

Theoretically and computationally describing the operation of nanodiodes requires characterizing the transitions between multiple electron emission mechanisms for nanodiodes with complicated geometries. This motivates our development of techniques to determine when simplified theories for individual mechanisms suffice compared to more complete, but more computationally expensive, models. Leveraging recent theories that define a canonical gap distance to translate planar theory to nonplanar diodes, we derive the conditions for the transitions among thermal emission, field emission, and space-charge-limited current density (SCLCD) in vacuum and with collisions for non-Cartesian coordinate systems, including spherical, cylindrical, and prolate spheroidal coordinate systems. Particle-in-cell (PIC) simulations of the current density as a function of applied voltage for a tip-to-plate geometry in vacuum agreed qualitatively with the asymptotes for thermal emission at low voltage and SCLCD at higher voltage using the canonical gap distance. As a result, this demonstrates the utility of this approach for guiding system design and suggests future extensions to save simulation time for more realistic geometries that are more computationally expensive.

Conformal mapping↗
NASA NTRS1977

Lift enhancement by an externally trapped vortex

A theoretical study is made of the performance capabilities of a lift concept that utilizes a spanwise vortex over the upper surface of the wing. The vortex is generated by a vertical flap near the leading edge of the wing and maintained by suction through orifices in endplates at the wingtip. The analysis approximates the three-dimensional flow field with a two-dimensional configuration that is mapped by conformal transformation into the flow about a circle. Theoretical solutions for a range of flap and orifice configurations predict that section lift coefficients up to around 10 can be achieved. It is concluded that such a lift concept is applicable to STOL aircraft if the vortex can be adequately stabilized and if the endplate suction can be generated efficiently.

Rossow, V. J.↗
NASA NTRS1977

Digital computer processing of LANDSAT data for North Alabama

Computer processing procedures and programs applied to Multispectral Scanner data from LANDSAT are described. The output product produced is a level 1 land use map in conformance with a Universal Transverse Mercator projection. The region studied was a five-county area in north Alabama.

Bond, A. D.↗
NASA NTRS2002

High-precision early mission narrow angle sciene with the Space Interferometry Mission

We have developed a technique that allows SIM to measure relative stellar positions with an accuracy of 1 micro-arcsecond at any time during its 5-yr mission. Unlike SIM's standard narrow-angle approach, Gridless Narrow Angle Astrometry (GNAA) does not rely on the global reference frame of grid stars that reaches full accuracy after 5 years. GNAA is simply the application of traditional single-telescope narrow angle techniques to SIM's narrow angle optical path delay measurements. In GNAA, a set of reference stars and a target star are observed at several baseline orientations. A linearized model uses delay measurements to solve for star positions and baseline orientations. A conformal transformation maps observations at different epochs to a common reference frame. The technique works on short period signals (P=days to months), allowing it to be applied to many of the known extra-solar planets, intriguing radio/X- ray binaries, and other periodic sources. The technique's accuracy is limited in the long-term by false acceleration due to a combination of reference star and target star proper motion. The science capability 1 micro-arcsecond astrometric precision - is unique to SIM.

Space Interferometry Mission↗
NASA NTRS1994

Optimum aerodynamic design via boundary control

These lectures describe the implementation of optimization techniques based on control theory for airfoil and wing design. In previous studies it was shown that control theory could be used to devise an effective optimization procedure for two-dimensional profiles in which the shape is determined by a conformal transformation from a unit circle, and the control is the mapping function. Recently the method has been implemented in an alternative formulation which does not depend on conformal mapping, so that it can more easily be extended to treat general configurations. The method has also been extended to treat the Euler equations, and results are presented for both two and three dimensional cases, including the optimization of a swept wing.

Jameson, Antony↗
NASA NTRS1994

Control theory based airfoil design for potential flow and a finite volume discretization

This paper describes the implementation of optimization techniques based on control theory for airfoil design. In previous studies it was shown that control theory could be used to devise an effective optimization procedure for two-dimensional profiles in which the shape is determined by a conformal transformation from a unit circle, and the control is the mapping function. The goal of our present work is to develop a method which does not depend on conformal mapping, so that it can be extended to treat three-dimensional problems. Therefore, we have developed a method which can address arbitrary geometric shapes through the use of a finite volume method to discretize the potential flow equation. Here the control law serves to provide computationally inexpensive gradient information to a standard numerical optimization method. Results are presented, where both target speed distributions and minimum drag are used as objective functions.

Reuther, J.↗