Search NASA⌕ Search

SEARCH · Search NASA

Results for “Bounded domains”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12

Distributed deformation and block rotation in three dimensions

A model is developed that attempts to explain distributed deformation, particularly the relationship between fault slip and rotation of faults and blocks in a 3D stress field. Regions of distributed deformation (such as Southern California) are organized in complex arrays of contemporaneously active block-faulted domains. A 3D block rotation model is proposed here that tracks the orientation of blocks and their bounding faults during rotation. It is shown how only one set of faults, preexisting and rotating in an irrotational strike-slip stress field, can account for the three major phases of deformation observed in the Western Transverse Range domain, Southern California.

Scotti, Oona↗

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Dual receptor-sites reveal the structural basis for hyperactivation of sodium channels by poison-dart toxin batrachotoxin

The poison dart toxin batrachotoxin is exceptional for its high potency and toxicity, and for its multifaceted modification of the function of voltage-gated sodium channels. By using cryogenic electron microscopy, we identify two homologous, but nonidentical receptor sites that simultaneously bind two molecules of toxin, one at the interface between Domains I and IV, and the other at the interface between Domains III and IV of the cardiac sodium channel. Together, these two bound toxin molecules stabilize α/π helical conformation in the S6 segments that gate the pore, and one of the bound BTX-B molecules interacts with the crucial Lys1421 residue that is essential for sodium conductance and selectivity via an apparent water-bridged hydrogen bond. Overall, our structure provides insight into batrachotoxin’s potency, efficacy, and multifaceted functional effects on voltage-gated sodium channels via a dual receptor site mechanism.

59 BASIC BIOLOGICAL SCIENCES↗

Illumination of serotonin transporter mechanism and role of the allosteric site

The serotonin transporter (SERT) terminates serotonin signaling by using sodium and chloride gradients to drive reuptake of serotonin into presynaptic neurons and is the target of widely used medications to treat neuropsychiatric disorders. Despite decades of study, the molecular mechanism of serotonin transport, the coupling to ion gradients, and the role of the allosteric site have remained elusive. Here, we present cryo–electron microscopy structures of SERT in serotonin-bound and serotonin-free states, in the presence of sodium or potassium, resolving all fundamental states of the transport cycle. From the SERT-serotonin complex, we localize the substrate-bound allosteric site, formed by an aromatic pocket positioned in the scaffold domain in the extracellular vestibule, connected to the central site via a short tunnel. Together with elucidation of multiple apo state conformations, we provide previously unseen structural understanding of allosteric modulation, demonstrating how SERT binds serotonin from synaptic volumes and promotes unbinding into the presynaptic neurons.

59 BASIC BIOLOGICAL SCIENCES↗

Control design for robust stability in linear regulators: Application to aerospace flight control

Time domain stability robustness analysis and design for linear multivariable uncertain systems with bounded uncertainties is the central theme of the research. After reviewing the recently developed upper bounds on the linear elemental (structured), time varying perturbation of an asymptotically stable linear time invariant regulator, it is shown that it is possible to further improve these bounds by employing state transformations. Then introducing a quantitative measure called the stability robustness index, a state feedback conrol design algorithm is presented for a general linear regulator problem and then specialized to the case of modal systems as well as matched systems. The extension of the algorithm to stochastic systems with Kalman filter as the state estimator is presented. Finally an algorithm for robust dynamic compensator design is presented using Parameter Optimization (PO) procedure. Applications in a aircraft control and flexible structure control are presented along with a comparison with other existing methods.

Yedavalli, R. K.↗

Characteristic microwave background distortions from collapsing domain wall bubbles

The magnitude and angular pattern of distortions of the microwave background are analyzed by collapsing spherical domain walls. A characteristic pattern of redshift distortions of red or blue spikes surrounded by blue discs was found. The width and height of a spike is related to the diameter and magnitude of the disc. A measurement of the relations between these quantities thus can serve as an unambiguous indicator for a collapsing spherical domain wall. From the redshift distortion in the blue discs an upper bound was found on the surface energy density of the walls sigma is less than or approximately 8 MeV cubed.

Goetz, Guenter↗

Signal Processing Variables for Optimization of Flaw Detection in Composites Using Ultrasonic Guided Wave Scanning

This study analyzes the effect of signal processing variables on the ability of the ultrasonic guided wave scan method at NASA Glenn Research Center to distinguish various flaw conditions in ceramic matrix composites samples. In the ultrasonic guided wave scan method, several time- and frequency-domain parameters are calculated from the ultrasonic guided wave signal at each scan location to form images. The parameters include power spectral density, centroid mean time, total energy (zeroth moment), centroid frequency, and ultrasonic decay rate. A number of signal processing variables are available to the user when calculating these parameters. These signal processing variables include 1) the time portion of the time-domain waveform processed, 2) integration type for the properties requiring integrations, 3) bounded versus unbounded integrations, 4) power spectral density window type, 5) and the number of time segments chosen if using the short-time fourier transform to calculate ultrasonic decay rate. Flaw conditions examined included delamination, cracking, and density variation.

Roth, Don J.↗

Multi-material ALE remap with interface sharpening using high-order matrix-free finite element methods

The arbitrary Lagrangian-Eulerian (ALE) technique involves remapping field quantities from a Lagrangian mesh to an optimized mesh in a conservative, accurate and bounds-preserving manner. For methods based on arbitrary order finite elements, as described in a reference, material volume fractions are advected in pseudo-time using flux-corrected transport (FCT) without any form of interface reconstruction. In practice, this can lead to excessive propagation of small volume fractions throughout the domain. In addition, this method requires assembly of a global advection matrix to compute the bounds-preserving low-order FCT solution. In this work, we introduce a new approach for ALE remap using a high-order matrix-free technique which incorporates a flux modification to sharpen material interfaces in a conservative manner. Our approach begins with computing a bounds-preserving low-order solution to the ALE remap equations at the element level. We then compute a sharp interface solution (not guaranteed to be bounds-preserving) which comes from solving an augmented version of the ALE remap equations with a conservative flux modification which acts to sharpen material volume fractions based on their gradients and transport directions. Using the sharp interface solution, we make global corrections to the bounds-preserving solution while maintaining preservation of bounds. By blending with the sharpened solution at the global level we are able to globally conserve mass without hindering the remap pseudo-time step. This new interface-aware ALE remap method is based entirely on partial assembly techniques where globally assembled matrix operators are no longer needed, resulting in a globally matrix-free FCT method for multi-material, multi-field ALE remap with high performance on GPU architectures. We present results of our new remap method on 1D, 2D and 3D benchmarks and describe the algorithmic tailoring for GPU architectures that was developed.

Vargas, Arturo [Lawrence Livermore National Labora↗

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site

Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA damage responses independent of the canonical SOS pathway. However, the molecular mechanisms by which DriD and other WYL-regulators sense environmental signals and recognize DNA are not well understood. We showed DriD DNA-binding is triggered by its interaction with ssDNA, which is produced during DNA damage. Here we describe the structure of the full-length C. crescentus DriD bound to both target DNA and effector ssDNA. DriD consists of an N-terminal winged-HTH (wHTH) domain, linker region, three-helix bundle, WYL-domain and C-terminal WCX-dimer domain. Strikingly, DriD binds DNA using a novel, asymmetric DNA-binding mechanism that results from different conformations adopted by the linker. Although the linker does not touch DNA, our data show that contacts it makes with the wHTH are key for specific DNA binding. The structure indicates how ssDNA-effector binding to the WYL-domain impacts wHTH DNA binding. In conclusion, we present the first structure of a WYL-activator bound to both effector and target DNA. The structure unveils a unique, asymmetric DNA binding mode that is likely conserved among WYL-activators.

59 BASIC BIOLOGICAL SCIENCES↗

Robust control design with real parameter uncertainty using absolute stability theory

The purpose of this thesis is to investigate an extension of mu theory for robust control design by considering systems with linear and nonlinear real parameter uncertainties. In the process, explicit connections are made between mixed mu and absolute stability theory. In particular, it is shown that the upper bounds for mixed mu are a generalization of results from absolute stability theory. Both state space and frequency domain criteria are developed for several nonlinearities and stability multipliers using the wealth of literature on absolute stability theory and the concepts of supply rates and storage functions. The state space conditions are expressed in terms of Riccati equations and parameter-dependent Lyapunov functions. For controller synthesis, these stability conditions are used to form an overbound of the H2 performance objective. A geometric interpretation of the equivalent frequency domain criteria in terms of off-axis circles clarifies the important role of the multiplier and shows that both the magnitude and phase of the uncertainty are considered. A numerical algorithm is developed to design robust controllers that minimize the bound on an H2 cost functional and satisfy an analysis test based on the Popov stability multiplier. The controller and multiplier coefficients are optimized simultaneously, which avoids the iteration and curve-fitting procedures required by the D-K procedure of mu synthesis. Several benchmark problems and experiments on the Middeck Active Control Experiment at M.I.T. demonstrate that these controllers achieve good robust performance and guaranteed stability bounds.

How, Jonathan P.↗

Evolution of the Cellulose Microfibril through Gamma-Valerolactone-Assisted Co-Solvent and Enzymatic Hydrolysis

Biomass recalcitrance during deconstruction remains a key bottleneck to affordable biomass processing technologies. A clear connection between the cell wall structure and biomass deconstruction is necessary to understand how lignocellulosic material is broken down to valuable monomeric components. Here, we monitor changes in the cellulose microfibril domains of poplar, sorghum, and switchgrass throughout gamma-valerolactone (GVL)–water co-solvent pretreatment and enzymatic hydrolysis using solid-state 13 C cross-polarization magic angle spinning nuclear magnetic resonance spectroscopy (CP/MAS 13 C-NMR) and wide-angle X-ray scattering (WAXS). Spectral fitting of NMR peaks corresponding to different cellulose microenvironments at the C 4 carbon center suggests that a mildly acidic GVL–water co-solvent pretreatment of poplar leads to nearly full removal of xylan–cellulose linkages, which primes the cellulose for enzymatic attack. The spectral fitting also suggests that the pretreatment causes significant depletion of the inaccessible fibril surface domains with an increase in more thermally stable crystalline resonances (I β ). WAXS confirmed a decrease in the lattice spacing between (200) crystalline planes with increasing co-solvent pretreatment severity. These results are interpreted as an opening of bound microfibril surfaces previously inaccessible to the co-solvent system, which leaves behind a more thermally stable, crystalline domain that is potentially prone to relaxation and recrystallization. Full conversion of residual GVL-pretreated biomass was achieved after the GVL co-solvent pretreatment at 140 °C using a commercial enzyme cocktail, CTec2, which contains different cellulases and other enzymes. Spectral fitting of enzymatically hydrolyzed samples by a single engineered cellulase, CelR, suggests that the residual cellulose recalcitrance is mainly due to the inability of CelR to digest the I β crystalline domain present in pretreated samples. This work helps to provide new information regarding the structure of the cell wall and recalcitrance throughout GVL–water mild acidolysis and CelR enzymatic biomass deconstruction by tracking the evolution of structural domains within the cellulose microfibril. This work further directs recommendations for improving the conversion and sugar yields in future studies. Finally, our findings inform inquiry into larger questions of cellulose recalcitrance through GVL pretreatment and CelR enzymatic hydrolysis and give insight into subsequent required steps for full cellulose conversion with attention to the most recalcitrant cellulose structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comparison of frequency domain design and l1-optimal control

A frequency-domain design methodology is applied to a DC motor-speed control system and the results are compared to those obtained using l1-optimal control theory (Pearson and Bamieh, 1990). Both methods synthesize controllers that maximize the allowable size of an unknown-but-bounded disturbance while satisfying prespecified constraints on the control, the control rate, and the outputs. The frequency-domain design technique in general results in much lower-order compensators than those required by the l1-optimal method for a given size of disturbance. Also, the design trade-offs regarding the bandwidth of the system, the size of the disturbance input, and the structural complexity of the controller transfer function become quite transparent.

Jayasuriya, Suhada↗

Rescheduling with iterative repair

This paper presents a new approach to rescheduling called constraint-based iterative repair. This approach gives our system the ability to satisfy domain constraints, address optimization concerns, minimize perturbation to the original schedule, produce modified schedules, quickly, and exhibits 'anytime' behavior. The system begins with an initial, flawed schedule and then iteratively repairs constraint violations until a conflict-free schedule is produced. In an empirical demonstration, we vary the importance of minimizing perturbation and report how fast the system is able to resolve conflicts in a given time bound. We also show the anytime characteristics of the system. These experiments were performed within the domain of Space Shuttle ground processing.

Zweben, Monte↗

Elucidating correlated defects in metal organic frameworks using theory-guided inelastic neutron scattering spectroscopy

Metal organic frameworks (MOFs) that incorporate metal oxide cluster nodes, exemplified by UiO-66, have been widely studied, especially in terms of their deviations from the ideal, defect-free crystalline structures. Although defects such as missing linkers, missing nodes, and the presence of adventitious synthesis-derived node ligands (such as acetates and formates) have been proposed, their exact structures remain unknown. Previously, it was demonstrated that defects are correlated and span multiple unit cells. The highly specialized techniques used in these studies are not easily applicable to other MOFs. Thus, there is a need to develop new experimental and computational approaches to understand the structure and properties of defects in a wider variety of MOFs. Here, we show how low-frequency phonon modes measured by inelastic neutron scattering (INS) spectroscopy can be combined with density functional theory (DFT) simulations to provide unprecedented insights into the defect structure of UiO-66. We are able to identify and assign peaks in the fingerprint region (<100 cm –1 ) which correspond to phonon modes only present in certain defective topologies. Specifically, this analysis suggests that our sample of UiO-66 consists of predominantly defect-free fcu regions with smaller domains corresponding to a defective bcu topology with 4 and 2 acetate ligands bound to the Zr 6 O 8 nodes. Importantly, the INS/DFT approach provides detailed structural insights (e.g., relative positions and numbers of acetate ligands) that are not accessible with microscopy-based techniques. Furthermore, the quantitative agreement between DFT simulations and the experimental INS spectrum combined with the relative simplicity of sample preparation, suggests that this methodology may become part of the standard and preferred protocol for the characterization of MOFs, and, in particular, for elucidating the structure defects in these materials.

36 MATERIALS SCIENCE↗

Solution of an eigenvalue problem for the Laplace operator on a spherical surface

Methods for obtaining approximate solutions for the fundamental eigenvalue of the Laplace-Beltrami operator (also referred to as the membrane eigenvalue problem for the vibration equation) on the unit spherical surface are developed. Two specific types of spherical surface domains are considered: (1) the interior of a spherical triangle, i.e., the region bounded by arcs of three great circles, and (2) the exterior of a great circle arc extending for less than pi radians on the sphere (a spherical surface with a slit). In both cases, zero boundary conditions are imposed. In order to solve the resulting second-order elliptic partial differential equations in two independent variables, a finite difference approximation is derived. The symmetric (generally five-point) finite difference equations that develop are written in matrix form and then solved by the iterative method of point successive overrelaxation. Upon convergence of this iterative method, the fundamental eigenvalue is approximated by iteration utilizing the power method as applied to the finite Rayleigh quotient.

Walden, H.↗

Shifting Between Compute and Memory Bounds: A Compression-Enabled Roofline Model

In the evolving landscape of high-performance computing, especially to fight the end of Moore’s Law and Dennard’s Scaling, the ability to shift between compute-bound and memory-bound states is critical for enhancing adaptability and flexibility to diverse system and domain-specific architectures. Such capability is vital for optimizing performance across distinguished hardware configurations, such as accelerators, memory hierarchies, and cache systems. Despite that ad hoc optimization techniques, such as compressed/approximate computation, have been enabled for compute-/data-intensive computing for improved performance in distinct hardware settings, there lacks an understanding of 1) the rational behind performance improvement; 2) capability of different optimizations; 3) what optimization to respond to specific computational and memory demands. This work proposes a compression-enabled roofline model to facilitate this adaptability with data compression techniques to balance and transform between computational and memory demands. This model enables applications to adjust in response to the specific strengths and limitations of the underlying hardware and system to optimize resource utilization. The effectiveness of this approach is demonstrated with matrix multiplication kernels on different input sizes, with turning on/off various compression techniques, including 1) low-precision floating point; 2) sparse matrix formulation; and 3) compressed arrays with ZFP. By reducing memory transfer volumes and cache misses and increasing data locality and computational intensity through compression, the specific roofline model can transform between compute and memory bounds to align more efficiently with system capabilities. This advancement not only improves overall performance but also maximizes adaptability in diverse computing environments.

Naraparaju, Ramasoumya [University of Washington]↗

Trellis complexity bounds for decoding linear block codes

We consider the problem of finding a trellis for a linear block code that minimizes one or more measures of trellis complexity. The domain of optimization may be different permutations of the same code or different codes with the same parameters. Constraints on trellises, including relationships between the minimal trellis of a code and that of the dual code, are used to derive bounds on complexity. We define a partial ordering on trellises: If a trellis is optimum with respect to this partial ordering, if has the desirable property that it simultaneously minimizes all of the complexity measures examined. We examine properties of such optimal trellises and give examples of optimal permutations of codes, most notably the (48,24,12) quadratic residue code.

Kiely, A. B.↗

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

59 BASIC BIOLOGICAL SCIENCES↗