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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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At least 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
NASA NTRS1987

Shape design sensitivity analysis and optimal design of structural systems

The material derivative concept of continuum mechanics and an adjoint variable method of design sensitivity analysis are used to relate variations in structural shape to measures of structural performance. A domain method of shape design sensitivity analysis is used to best utilize the basic character of the finite element method that gives accurate information not on the boundary but in the domain. Implementation of shape design sensitivty analysis using finite element computer codes is discussed. Recent numerical results are used to demonstrate the accuracy obtainable using the method. Result of design sensitivity analysis is used to carry out design optimization of a built-up structure.

Choi, Kyung K.↗
DOE OSTI2025

Autonomous Multistate Nanoencoding Using Combinatorial Ferroelectric Closure Domains in BiFeO 3

Recent advances in ferroic materials have identified topological defects as promising candidates for enabling additional functionalities in future electronic systems. The generation of stable and customizable polar topologies is needed to achieve multistates that enable beyond-binary device architectures. Here, in this study, we show how to autonomously pattern on-demand highly tunable striped closure domains in pristine rhombohedral-phase BiFeO 3 thin films through precise scanning of a biased atomic force microscopy tip along carefully designed paths. By employing this strategy, we generate and manipulate closed-loop structures with high spatial resolution in an automated manner, allowing the creation of highly tunable and intricate topological domain structures that exhibit distinct polarization configurations without the need for electrode deposition or complex heterostructure growth. As a proof-of-concept for ferroelectric beyond-binary memory devices, we use such topological domains as multistates, engineering an alphabet and automating the symbolic writing/reading process using autonomous microscopy. The resulting information density is compared with that of current commercially available memory devices, demonstrating the potential of ferroelectric topological domains for multistate information storage applications.

BiFeO3↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2017

Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

Central to CD8+ T cell–mediated immunity is the recognition of peptide–major histocompatibility complex class I (p–MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein–related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface

Clostridium difficile is a clinically significant pathogen that causes mild-to-severe (and often recurrent) colon infections. Disease symptoms stem from the activities of two large, multidomain toxins known as TcdA and TcdB. The toxins can bind, enter, and perturb host cell function through a multistep mechanism of receptor binding, endocytosis, pore formation, autoproteolysis, and glucosyltransferase-mediated modification of host substrates. Monoclonal antibodies that neutralize toxin activity provide a survival benefit in preclinical animal models and prevent recurrent infections in human clinical trials. However, the molecular mechanisms involved in these neutralizing activities are unclear. To this end, we performed structural studies on a neutralizing monoclonal antibody, PA50, a humanized mAb with both potent and broad-spectrum neutralizing activity, in complex with TcdA. Electron microscopy imaging and multiangle light-scattering analysis revealed that PA50 binds multiple sites on the TcdA C-terminal combined repetitive oligopeptides (CROPs) domain. A crystal structure of two PA50 Fabs bound to a segment of the TcdA CROPs helped define a conserved epitope that is distinct from previously identified carbohydrate-binding sites. Binding of TcdA to the host cell surface was directly blocked by either PA50 mAb or Fab and suggested that receptor blockade is the mechanism by which PA50 neutralizes TcdA. These findings highlight the importance of the CROPs C terminus in cell-surface binding and a role for neutralizing antibodies in defining structural features critical to a pathogen's mechanism of action. We conclude that PA50 protects host cells by blocking the binding of TcdA to cell surfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Efficient derivative computation for unsteady fatigue-constrained nonlinear aero-structural wind turbine blade optimization

Gradient-based optimization offers significant efficiency advantages for wind turbine blade design, but its application has often been limited by the cost and accuracy of finite-difference derivative calculations, especially when fatigue constraints are considered. In this work, we systematically compare and evaluate four differentiation techniques, namely algorithmic differentiation, implicit differentiation, sparsity exploitation, and parallelization, to determine their effectiveness in computing accurate gradients through time-domain aero-structural simulations. By integrating these techniques with unsteady nonlinear aerodynamic and structural models, we develop software designed for accurate gradient computation. We show that combining these techniques addresses memory and runtime challenges associated with long simulations required by design load cases. Specifically, the most effective combination reduces derivative computation wall time by over an order of magnitude compared to finite differencing while maintaining superior accuracy. We demonstrate this approach in a proof-of-concept aero-structural optimization of a wind turbine blade that improves the cost of energy by 12.78 %. This comparative study establishes a viable approach for fatigue-aware blade design that balances computational efficiency with modeling accuracy.

17 WIND ENERGY↗
DOE OSTI2016

Crystal structure and interaction studies of the human FBxo3 ApaG domain

Transcriptional activation of proinflammatory cytokines, mediated by tumor necrosis factor receptor-associated factors (TRAFs), is in part triggered by the degradation of the F-box protein, FBxl2, via an E3 ligase that contains another F-box protein, FBxo3. The ApaG domain of FBxo3 is required for the interaction with and degradation of FBxl2 [Mallampalli RK et al., (2013) J Immunol 191, 5247–5255]. Here, we report the X-ray structure of the human FBxo3 ApaG domain, residues 278–407, at 2.0 Å resolution. Like bacterial ApaG proteins, this domain is characterized by a classic Immunoglobin/Fibronectin III-type fold, comprising a seven-stranded β-sheet core, surrounded by four extended loops. Although cation binding had been proposed for bacterial ApaG proteins, no interactions with Mg 2+ or Co 2+ were detected for the human ApaG domain. In addition, dinucleotide polyphosphates, which have been reported to be second messengers in the inflammation response and targets of the bacterial apaG-containing operon, are not bound by the human ApaG domain. In the context of the full-length protein, loop 1, comprising residues 294-303, is critical for the interaction with FBxl2. However, titration of the individual ApaG domain with a 15-mer FBxl2 peptide that was phosphorylated on the crucial T404, as well as the inability of the ApaG domain to interact with full-length FBxl2, assessed by coimmunoprecipitation, indicate that the ApaG domain alone is necessary, but not sufficient for binding and degradation of FBxl2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data Driven Correlated Noise Simulation for the ICEBERG LArTPC

Accurate electronic-noise simulation is essential for low-energy physics in liquid-argon TPCs. More realistic noise modeling allows us to better tune reconstruction algorithms and more reliably assess and optimize signal-detection thresholds. We present a data-driven noise simulation framework developed for the ICEBERG test stand for DUNE that generates synthetic noise waveforms that reproduce both (i) the measured per-channel magnitude of the Fast Fourier Transform (FFT) and (ii) frequency-dependent channel-to-channel correlations observed in ICEBERG noise data. Using a dedicated noise-only dataset, we build a compact noise model containing per-channel FFT-magnitude targets together with a small set of band-wise cross-wire color matrices. White noise is generated in the frequency domain by drawing circular-symmetric complex Gaussian coefficients with random phases and scaling them to match the measured FFT-magnitude targets, and cross-wire correlations are subsequently imposed using the stored color matrices. The model and algorithm were integrated into the LArSoft + Wire-Cell Toolkit simulation chain and validated by comparing waveform structure, frequency-domain spectra, and band-limited correlation matrices from simulated noise and ICEBERG data. This approach can be extended to other LArTPC operating conditions.

Ghosh, Avik [Iowa State U.]↗
DOE OSTI2017

Molecular weight dependence of carrier mobility and recombination rate in neat P3HT films

The microstructure dependence of carrier mobility and recombination rates of neat films of poly 3-hexylthyophene (P3HT) were determined for a range of materials of weight-average molecular weights, Mw, ranging from 14 to 331 kDa. This variation has previously been shown to modify the polymer microstructure, with low molecular weights forming a one-phase, paraffinic-like structure comprised of chain-extended crystallites, and higher molecular weights forming a semicrystalline structure with crystalline domains being embedded in an amorphous matrix. Using Charge Extraction by Linearly Increasing Voltage (CELIV), we show here that the carrier mobility in P3HT devices peaks for materials of Mw = 48 kDa, and that the recombination rate decreases monotonically with increasing molecular weight. This trend is likely due to the development of a semicrystalline, two-phase structure with increasing Mw, which allows for the spatial separation of holes and electrons into the amorphous and crystalline regions, respectively. This separation leads to decreased recombination.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Autoregulation of the LIM kinases by their PDZ domain

LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the ‘x-Φ-G-Φ’ motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases

Despite the importance of plant lignans and isoflavonoids in human health protection (e.g. for both treatment and prevention of onset of various cancers) as well as in plant biology (e.g. in defense functions and in heartwood development), systematic studies on the enzymes involved in their biosynthesis have only recently begun. In this investigation, three NADPH-dependent aromatic alcohol reductases were comprehensively studied, namely pinoresinol-lariciresinol reductase (PLR), phenylcoumaran benzylic ether reductase (PCBER), and isoflavone reductase (IFR), which are involved in central steps to the various important bioactive lignans and isoflavonoids. Of particular interest was in determining how differing regio- and enantiospecificities are achieved with the different enzymes, despite each apparently going through similar enone intermediates. Initially, the three-dimensional x-ray crystal structures of both PLR_Tp1 and PCBER_Pt1 were solved and refined to 2.5 and 2.2 A resolutions, respectively. Not only do they share high gene sequence similarity, but their structures are similar, having a continuous alpha/beta NADPH-binding domain and a smaller substrate-binding domain. IFR (whose crystal structure is not yet obtained) was also compared (modeled) with PLR and PCBER and was deduced to have the same overall basic structure. The basis for the distinct enantio-specific and regio-specific reactions of PCBER, PLR, and IFR, as well as the reaction mechanism and participating residues involved (as identified by site-directed mutagenesis), are discussed.

NASA Discipline Plant Biology↗
DOE OSTI2022

Unveiling the Emergent Traits of Chiral Spin Textures in Magnetic Multilayers

Abstract Magnetic skyrmions are topologically wound nanoscale textures of spins whose ambient stability and electrical manipulation in multilayer films have led to an explosion of research activities. While past efforts focused predominantly on isolated skyrmions, recently ensembles of chiral spin textures, consisting of skyrmions and magnetic stripes, are shown to possess rich interactions with potential for device applications. However, several fundamental aspects of chiral spin texture phenomenology remain to be elucidated, including their domain wall (DW) structure, thermodynamic stability, and morphological transitions. Here the evolution of these textural characteristics are unveiled on a tunable multilayer platform—wherein chiral interactions governing spin texture energetics can be widely varied—using a combination of full‐field electron and soft X‐ray microscopies with numerical simulations. With increasing chiral interactions, the emergence of Néel helicity, followed by a marked reduction in domain compressibility, and finally a transformation in the skyrmion formation mechanism are demonstrated. Together with an analytical model, these experiments establish a comprehensive microscopic framework for investigating and tailoring chiral spin texture character in multilayer films.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Crystal structures of Ca 2+ –calmodulin bound to Na V C-terminal regions suggest role for EF-hand domain in binding and inactivation

Voltage-gated sodium (Na V ) and calcium channels (Ca V ) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca 2+ -occupied CaM, bound to the CT of Na V 1.5. The structure shows that the C-terminal lobe binds to a site ~90° rotated relative to a previous site reported for an apoCaM complex with the Na V 1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca 2+ -occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca 2+ -free and Ca 2+ -occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related Na V 1.4 channel has been shown to undergo Ca 2+ -dependent inactivation (CDI) akin to Ca V s. We present a crystal structure of Ca 2+ /CaM bound to the Na V 1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structural basis of HIV-1 capsid recognition by PF74 and CPSF6

Upon infection of susceptible cells by HIV-1, the conical capsid formed by ~250 hexamers and 12 pentamers of the CA protein is delivered to the cytoplasm. In this study, the capsid shields the RNA genome and proteins required for reverse transcription. In addition, the surface of the capsid mediates numerous host–virus interactions, which either promote infection or enable viral restriction by innate immune responses. In the intact capsid, there is an intermolecular interface between the N-terminal domain (NTD) of one subunit and the C-terminal domain (CTD) of the adjacent subunit within the same hexameric ring. The NTD–CTD interface is critical for capsid assembly, both as an architectural element of the CA hexamer and pentamer and as a mechanistic element for generating lattice curvature. Here we report biochemical experiments showing that PF-3450074 (PF74), a drug that inhibits HIV-1 infection, as well as host proteins cleavage and polyadenylation specific factor 6 (CPSF6) and nucleoporin 153 kDa (NUP153), bind to the CA hexamer with at least 10-fold higher affinities compared with nonassembled CA or isolated CA domains. The crystal structure of PF74 in complex with the CA hexamer reveals that PF74 binds in a preformed pocket encompassing the NTD–CTD interface, suggesting that the principal inhibitory target of PF74 is the assembled capsid. Likewise, CPSF6 binds in the same pocket. Given that the NTD–CTD interface is a specific molecular signature of assembled hexamers in the capsid, binding of NUP153 at this site suggests that key features of capsid architecture remain intact upon delivery of the preintegration complex to the nucleus.

59 BASIC BIOLOGICAL SCIENCES↗