SEARCH · Engineering Papers
Results for “DOMAIN STRUCTURE”
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.
High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3
Explore the source record for details and available documents.
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil
The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1–GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1–GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.
The Crystal Structure of the Ubiquitin-like Domain of Ribosome Assembly Factor Ytm1 and Characterization of Its Interaction with the AAA-ATPase Midasin
The synthesis of eukaryotic ribosomes is a complex, energetically demanding process requiring the aid of numerous non-ribosomal factors, such as the PeBoW complex. The mammalian PeBoW complex, composed of Pes1, Bop1, and WDR12, is essential for the processing of the 32S preribosomal RNA. Previous work in Saccharomyces cerevisiae has shown that release of the homologous proteins in this complex (Nop7, Erb1, and Ytm1, respectively) from preribosomal particles requires Rea1 (midasin or MDN1 in humans), a large dynein-like protein. Midasin contains a C-terminal metal ion-dependent adhesion site (MIDAS) domain that interacts with the N-terminal ubiquitin-like (UBL) domain of Ytm1/WDR12 as well as the UBL domain of Rsa4/Nle1 in a later step in the ribosome maturation pathway. Here we present the crystal structure of the UBL domain of the WDR12 homologue from S. cerevisiae at 1.7 Å resolution and demonstrate that human midasin binds to WDR12 as well as Nle1 through their respective UBL domains. Midasin contains a well conserved extension region upstream of the MIDAS domain required for binding WDR12 and Nle1, and the interaction is dependent upon metal ion coordination because removal of the metal or mutation of residues that coordinate the metal ion diminishes the interaction. Mammalian WDR12 displays prominent nucleolar localization that is dependent upon active ribosomal RNA transcription. Here, based upon these results, we propose that release of the PeBoW complex and subsequent release of Nle1 by midasin is a well conserved step in the ribosome maturation pathway in both yeast and mammalian cells.
Interdomain region in single-crystal lithium niobate bimorph actuators produced by light annealing
The interdomain region of a bidomain strucrture formed in 127°-cut lithium niobate single crystals using light annealing has been studied by optical and scanning probe microscopies. A periodic subdomain structure on the 180° macrodomain wall is visualized by piezoresponse force microscopy. The piezoresponse signal (polarization) is shown to be a power-law function of the domain width with an exponent n = 0.53.
Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin
The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through the adaptor protein ankyrin, which directly bridges the interaction between {beta}-spectrin and membrane proteins. Ankyrins have a modular structure that includes two tandem ZU5 domains. The first domain, ZU5A, is directly responsible for binding {beta}-spectrin. Here, we present a structure of the tandem ZU5 repeats of human erythrocyte ankyrin. Structural and biophysical experiments show that the second ZU5 domain, ZU5B, does not participate in spectrin binding. ZU5B is structurally similar to the ZU5 domain found in the netrin receptor UNC5b supramodule, suggesting that it could interact with other domains in ankyrin. Comparison of several ZU5 domains demonstrates that the ZU5 domain represents a compact and versatile protein interaction module.
Structural diversity and clustering of bacterial flagellar outer domains
Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
Domain-dependent strain and stacking in two-dimensional van der Waals ferroelectrics
Van der Waals (vdW) ferroelectrics have attracted significant attention for their potential in next-generation nano-electronics. Two-dimensional (2D) group-IV monochalcogenides have emerged as a promising candidate due to their strong room temperature in-plane polarization down to a monolayer limit. However, their polarization is strongly coupled with the lattice strain and stacking orders, which impact their electronic properties. Here, we utilize four-dimensional scanning transmission electron microscopy (4D-STEM) to simultaneously probe the in-plane strain and out-of-plane stacking in vdW SnSe. Specifically, we observe large lattice strain up to 4% with a gradient across ~50 nm to compensate lattice mismatch at domain walls, mitigating defects initiation. Additionally, we discover the unusual ferroelectric-to-antiferroelectric domain walls stabilized by vdW force and may lead to anisotropic nonlinear optical responses. Our findings provide a comprehensive understanding of in-plane and out-of-plane structures affecting domain properties in vdW SnSe, laying the foundation for domain wall engineering in vdW ferroelectrics.
Thin film confinement reduces compatibility in symmetric ternary block copolymer/homopolymer blends
Here, the thin film phase behavior of ternary blends consisting of symmetric poly(styrene) (PS)– b –poly(dimethylsiloxane)(PDMS), PS, and PDMS was investigated using X–ray reflectivity (XRR) and atomic force microscopy (AFM). This system is strongly segregated, and the homopolymers are approximately the same length as the corresponding blocks of the copolymer. The XRR and AFM data are used to quantify changes in domain spacing ( L ) and morphology evolution with increasing homopolymer content (Φ H ). In 100 nm thick films, from Φ H = 0 to 0.20, the system maintains a perfect parallel lamellar structure and domains swell as predicted based on theory; however, from Φ H = 0.30 to 0.50, a morphology transition to a “dot pattern” morphology (tentatively identified as perforated lamellae) and mixed morphologies were observed before macrophase separation. In thicker films, dot patterns were observed for a broad range of Φ H before macrophase separation. The absence of the bicontinuous microemulsion phase reported for bulk blends and thin films of perpendicular lamellae and the presence of dot patterns/perforated lamellae are attributed to preferential migration of the PDMS homopolymer to the wetting layers located at the substrate and free air interfaces, which leads to an asymmetric composition within the film and morphology transition.
Lifshitz metal–insulator transition induced by the all-in/all-out magnetic order in the pyrochlore oxide Cd{sub 2}Os{sub 2}O{sub 7}
We investigate the metal–insulator transition (MIT) of the osmium pyrochlore oxide Cd{sub 2}Os{sub 2}O{sub 7} through transport and magnetization measurements. The MIT and a magnetic transition to the all-in/all-out (AIAO) order occur simultaneously at 227 K. We propose a mechanism based on a Lifshitz transition induced by the AIAO magnetic order probably via strong spin–orbit couplings in the specific semimetallic band structure. It is suggested, moreover, that two observed puzzles, a finite conductivity near T = 0 and an emergence of weak ferromagnetic moments, are not bulk properties but originate at magnetic domain walls between two kinds of AIAO domains.
Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition
Contact-dependent growth inhibition (CDI) is a widespread form of inter-bacterial competition mediated by CdiA effector proteins. CdiA is presented on the inhibitor cell surface and delivers its toxic C-terminal region (CdiA-CT) into neighboring bacteria upon contact. Inhibitor cells also produce CdiI immunity proteins, which neutralize CdiA-CT toxins to prevent auto-inhibition. Here, we describe a diverse group of CDI ionophore toxins that dissipate the transmembrane potential in target bacteria. These CdiA-CT toxins are composed of two distinct domains based on AlphaFold2 modeling. The C-terminal ionophore domains are all predicted to form five-helix bundles capable of spanning the cell membrane. The N-terminal "entry" domains are variable in structure and appear to hijack different integral membrane proteins to promote toxin assembly into the lipid bilayer. The CDI ionophores deployed by E. coli isolates partition into six major groups based on their entry domain structures. Comparative sequence analyses led to the identification of receptor proteins for ionophore toxins from groups 1 & 3 (AcrB), group 2 (SecY) and groups 4 (YciB). Using forward genetic approaches, we identify novel receptors for the group 5 and 6 ionophores. Group 5 exploits homologous putrescine import proteins encoded by puuP and plaP, and group 6 toxins recognize di/tripeptide transporters encoded by paralogous dtpA and dtpB genes. Finally, we find that the ionophore domains exhibit significant intra-group sequence variation, particularly at positions that are predicted to interact with CdiI. Accordingly, the corresponding immunity proteins are also highly polymorphic, typically sharing only ~30% sequence identity with members of the same group. Competition experiments confirm that the immunity proteins are specific for their cognate ionophores and provide no protection against other toxins from the same group. The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.
A 3.4-Å cryo-electron microscopy structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles
Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV-1 and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other sites, as well as different glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. Overall, this structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.
Spin orbit torque in ferromagnet/topological-quantum-material heterostructures
The main objective of this proposal was to investigate the spin-orbital driven phenomena in topological insulator (TI)/ferromagnet (FM) or transition metal (TM) heterostructures. In particularly, we tried to utilize the spin-momentum locking properties on the surface of TIs to achieve ideal spin-orbit torques (SOTs). In practice, we found that the surface properties have been greatly modified, resulting in much more complicated magneto-transport behaviors than what is expected in SOT-driven magnetotransport. Through systematic and extended investigations, we start to unravel that the nonlinear magnetotransport properties, which was, in the past, mainly attributed to SOT-driven phenomena, can be used to infer the modification of the electronic band structures of TIs and spin textures in FMs which are closely related with charge-spin interconversion phenomena. Regarding the band structures In TIs, we find under electrostatic perturbations imposed by deposition of nonmagnetic TMs, the quantum well states formed on the surface of TIs develop substantial Rashba spin-splitting, which is detected as a bilinear magnetoresistance (BMR). Under magnetic perturbations, the nonlinear planar Hall effect (NPHE) in the topological surface states is greatly enhanced, possibly reflecting the modified surface band structure due to time-reversal symmetry breaking. In a double HM/FM heterostructure where the magnetic anisotropy can be robustly tuned, we observed second-harmonic Hall voltage responses corresponding to domain wall structures with fixed chirality, stabilized by interfacial Dzyaloshinskii–Moriya interaction (DMI). In addition, in the linear transport regime, we utilized inverse-SHE-induced anomalous Hall effect in Pt to probe the exchange bias on the surface of a doped magnetic insulator Tm 3 Fe 5 O 12 .
Grid generation for computational CFD of full aerodynamic configurations
It is now possible to compute flow about very complex three-dimensional aerodynamic configurations. Grid generation is an essential part of such computations and a basic capability has been demonstrated. The present problems are: (1) choosing among the competing approaches (structured, unstructured or rectangular); (2) automating and packaging software for grid generation; (3) assessing and assuring grid quality; (4) solid boundary-surface representation and grid generation on solid boundaries; (5) automated domain decomposition (structured grids); (6) grid adaption during the flow solution process. This paper discusses some of the capabilities in the computation of complex three-dimensional grids and addresses some of he current challenges.
Discovery of spontaneous mesoscopic strain waves in nematic domains using dark-field x-ray microscopy
Electronic nematic order arises when correlated electrons spontaneously break the rotational symmetry of a crystal lattice. When electronic nematic order couples bilinearly to symmetry-breaking lattice strain, both appear together at a single ferroelastic phase transition, producing structural twin domains with distinct orientations of the nematic director. While the effects of applied strain on these domains are well established, the intrinsic behavior of spontaneous subdomain strain fields has remained unexplored. Here, we report the discovery of spontaneous mesoscopic strain waves within individual nematic domains of an iron-based superconductor, observed using dark-field x-ray microscopy (DFXM). Using this advanced full-field imaging technique, we visualize subdomain strain modulations emerging concurrently with nematic order. Elastic compatibility relations governing inhomogeneous strains provide a natural mechanism for the strain waves. Our findings reveal a broadly relevant form of strain self-organization and position DFXM as a powerful probe of the local interplay between lattice strain and electronic order.
Investigation on properties of ultrafast switching in a bulk gallium arsenide avalanche semiconductor switch
Properties of ultrafast switching in a bulk gallium arsenide (GaAs) avalanche semiconductor switch based on semi-insulating wafer, triggered by an optical pulse, were analyzed using physics-based numerical simulations. It has been demonstrated that when a voltage with amplitude of 5.2 kV is applied, after an exciting optical pulse with energy of 1 μJ arrival, the structure with thickness of 650 μm reaches a high conductivity state within 110 ps. Carriers are created due to photons absorption, and electrons and holes drift to anode and cathode terminals, respectively. Static ionizing domains appear both at anode and cathode terminals, and create impact-generated carriers which contribute to the formation of electron-hole plasma along entire channel. When the electric field in plasma region increases above the critical value (∼4 kV/cm) at which the electrons drift velocity peaks, a domain comes into being. An increase in carrier concentration due to avalanche multiplication in the domains reduces the domain width and results in the formation of an additional domain as soon as the field outside the domains increases above ∼4 kV/cm. The formation and evolution of multiple powerfully avalanching domains observed in the simulations are the physical reasons of ultrafast switching. The switch exhibits delayed breakdown with the characteristics affected by biased electric field, current density, and optical pulse energy. The dependence of threshold energy of the exciting optical pulse on the biased electric field is discussed.
Magnetic field dependence of nonlinear magnetic response and tricritical point in the monoaxial chiral helimagnet Cr 1 / 3 Nb S 2
We present a comprehensive study of the magnetization dynamics and phase evolution in the chiral helimagnet Cr 1/3 NbS 2 , which realizes a chiral soliton lattice (CSL). The magnetic field dependence of the ac magnetic response is analyzed for the first five harmonic components, M nω (H ) (n = 1–5), using a phase sensitive measurement over a frequency range, f = 11–10 000 Hz. At a critical field, the modulated CSL continuously evolves from a helicity-rich to a ferromagnetic domain-rich structure, where the crossover is revealed by the onset of an anomalous nonlinear magnetic response that coincides with extremely slow dynamics. The behavior is indicative of the formation of a spatially coherent array of large ferromagnetic domains, which relax on macroscopic time scales. The frequency dependence of the ac magnetic loss displays an asymmetric distribution of relaxation times across the highly nonlinear CSL regime, which shift to shorter time scales with increasing temperature. We experimentally resolve the tricritical point at T TCP in a temperature regime above the ferromagnetic Curie temperature which separates the linear and nonlinear magnetic regimes of the CSL at the phase transition. A comprehensive phase diagram is constructed which summarizes the features of the field and temperature dependence of the magnetic crossovers and phase transitions in Cr 1/3 NbS 2 .