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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Linking Domain Structure Evolution at a Grain Boundary to Piezoelectric Response via Nano‐Diffraction

Electric-field-induced domain structure switching in a 1 𝜇⁢m -thick Pb 0.99 (Zr 0.45 Ti 0.55 ) 0.98 Nb 0.02 O 3 (Nb-doped PZT) bicrystal film was characterized in situ via nano-focused synchrotron diffraction. The epitaxial film was deposited on a (100) SrTiO 3 bicrystal substrate. The changes in domain structure were mapped within a 5 𝜇⁢m × 5 𝜇⁢m area at and around an in-plane tilt-type (23.6°) grain boundary with 50 nm spatial resolution. Rocking curves collected at each point of the mapped area provided the ability to reconstruct spatially-varying three-dimensional (3D) reciprocal space maps around the grain boundary. The 3D reciprocal space maps reveal how different tilted 𝑎 -type domain variants interact with the grain boundary as a function of increasing electric field. Initially, a subset of 𝑎 -type domain variants with their polarization vectors largely orthogonal to the grain boundary were found in greater abundance within 570 nm of the grain boundary, possibly due to X-ray beam-induced local increases in the electrical conductivity, but after the coercive field was exceeded, reconfiguration of the ferroelastic domains was observed. The spatially-varying reciprocal space maps also facilitated evaluation of the strain field across the mapped area, along with 𝑑 33,𝑓 . Significant spatial heterogeneity of strain and 𝑑 33,𝑓 are observed, especially at the coercive field, which was attributed to maintaining deformation compatibility and correlated ferroelastic switching.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin

Iron is an important micronutrient that is required by bacteria to proliferate and to cause disease. Many bacterial pathogens forage iron from human hemoglobin (Hb) during infections, which contains this metal within heme (iron–protoporphyrin IX). Several clinically important pathogenic species within the Firmicutes phylum scavenge heme using surface-displayed or secreted NEAr Transporter (NEAT) domains. In this review, we discuss how these versatile proteins function in the Staphylococcus aureus Iron-regulated surface determinant system that scavenges heme-iron from Hb. S. aureus NEAT domains function as either Hb receptors or as heme-binding chaperones. In vitro studies have shown that heme-binding NEAT domains can rapidly exchange heme amongst one another via transiently forming transfer complexes, leading to the interesting hypothesis that they may form a protein-wire within the peptidoglycan layer through which heme flows from the microbial surface to the membrane. In Hb receptors, recent studies have revealed how dedicated heme- and Hb-binding NEAT domains function synergistically to extract Hb’s heme molecules, and how receptor binding to the Hb-haptoglobin complex may block its clearance by macrophages, prolonging microbial access to Hb’s iron. The functions of NEAT domains in other Gram-positive bacteria are also reviewed.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

A complex ligase ribozyme evolved in vitro from a group I ribozyme domain

Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.

NASA Discipline Exobiology↗
DOE OSTI2021

Confronting Domain Shift in Trained Neural Networks

Neural networks (NNs) are known as universal function approximators and can interpolate nonlinear functions between observed data points. However, when the target domain for deployment shifts from the training domain and NNs must extrapolate, the results are notoriously poor. Prior work Martinez et al. (2019) has shown that NN uncertainty estimates can be used to correct binary predictions in shifted domains without retraining the model. We hypothesize that this approach can be extended to correct real-valued time series predictions. As an exemplar, we consider two mechanical systems with nonlinear dynamics. The first system consists of a spring-mass system where the stiffness changes abruptly, and the second is a real experimental system with a frictional joint that is an open challenge for structural dynamicists to model efficiently. Our experiments will test whether 1) NN uncertainty estimates can identify when the input domain has shifted from the training domain and 2) whether the information used to calculate uncertainty estimates can be used to correct the NN’s time series predictions. While the method as proposed did not significantly improve predictions, our results did show potential for modifications that could improve models’ predictions and play a role in structural health monitoring systems that directly impact public safety.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Full-Wave and Circuit-Based Simulations of Cable Insulation Aging/Damage Using Time-Frequency Domain Reflectometry

This paper presents a combined full-wave and circuit-based simulation study to investigate the important topic of cable insulation aging and physical damage. The analysis employs the time-frequency domain reflectometry (TFDR) technique that combines the advantages of both time domain reflectometry (TDR) and frequency domain reflectometry (FDR) for improved location identification and feature resolution. Coaxial cable sections with a location containing insulation aging or physical damage are simulated using Ansys High Frequency Structure Simulator (HFSS). Simulated scattering (S) parameters are then imported into the Advanced Design System (ADS) solver for time domain simulation where a Gaussian windowed chirp signal or ‘chirplet’ is launched. Finally, continuous wavelet transform (CWT) is applied in MATLAB to perform time-frequency analysis of the reflected waveforms. The results reveal that a small change in the relative permittivity of the insulation or the presence of a small point of physical damage on the insulation is reflected as a considerable change in the CWT magnitude demonstrating the efficacy of the method.

cable aging, Non Destructive Examination, time-fre↗
DOE OSTI2025

Terrace‐Edge‐Induced Domain Nucleation in Room‐Temperature 2D Magnetic Van Der Waals Heterostructures

Abstract Terrace‐edges, which are step‐like height discontinuities formed during layer stacking or exfoliation, can locally modify magnetic characteristics. Magnetic domain behavior and its structural dependence in a 2D van der Waals (vdW) heterostructure composed of two distinct room‐temperature ferromagnets: Fe 3 GaTe 2 , an intrinsic vdW ferromagnet, and vanadium‐doped WSe 2 , a transition metal dichalcogenide exhibiting defect‐induced magnetism, is investigated. Using magnetic transmission X‐ray microscopy, the formation and annihilation of magnetic domains are directly observed and it is found that domains preferentially form at terrace‐edges of the heterostructure. Micromagnetic simulations reveal that in‐plane magnetization tilting near the terrace‐edge results in a localized maximum in total magnetic energy that promotes domain formation. The findings highlight the significant role of structural edge features and interfacial magnetic interactions in determining domain formation in hybrid 2D vdW magnetic systems, offering a new route to spatially controlled magnetization at room temperature.

Lee, Jieun↗
DOE OSTI2020

The C‐Terminal Domain of α‐Synuclein Confers Steric Stabilization on Synaptic Vesicle‐Like Surfaces

Abstract While α‐synuclein, an intrinsically disordered protein linked to Parkinson's disease, has been shown to associate with membrane organelles, its overall cellular function remains nebulous. α‐Synuclein binds to membranes through its amino‐terminal domain (first ≈100 residues), but there is no consensus on the biophysical function of the carboxyl‐terminal domain (last ≈40 residues) due, in part, to its lack of strong interaction partners and persisting intrinsic disorder even when membrane bound. Here, by directly applying force on α‐synuclein bound to spherical nanoparticle‐supported lipid bilayers (SSLBs) and tracking higher‐order structural changes through small‐angle X‐ray scattering, strong evidence is presented that α‐synuclein sterically stabilizes membrane surfaces through its carboxyl‐terminal domain. Full‐length α‐synuclein dramatically increases the critical osmotic pressure at which SSLBs cluster ( P C ≈ 1.3 × 10 5 Pa) compared to α‐synuclein without the carboxyl‐terminal domain ( P C ≈ 1.9 × 10 4 Pa) at physiological salt and temperature conditions. This clustering of α‐synuclein‐bound SSLBs is shown to be reversible and sensitive to monovalent/divalent salt, both features of grafted polyelectrolyte‐mediated steric stabilization. In elucidating the biophysical function of α‐synuclein in the framework of polymer science, it is demonstrated that the carboxyl‐terminal domain can potentially utilize its persisting intrinsic disorder to functionalize membrane surfaces.

Chung, Peter J.↗
DOE OSTI2021

A general framework for substructuring‐based domain decomposition methods for models having nonlocal interactions

Abstract A mathematical framework is provided for a substructuring‐based domain decomposition (DD) approach for nonlocal problems that features interactions between points separated by a finite distance. Here, by substructuring it is meant that a traditional geometric configuration for local partial differential equation (PDE) problems is used in which a computational domain is subdivided into non‐overlapping subdomains. In the nonlocal setting, this approach is substructuring‐based in the sense that those subdomains interact with neighboring domains over interface regions having finite volume, in contrast to the local PDE setting in which interfaces are lower dimensional manifolds separating abutting subdomains. Key results include the equivalence between the global, single‐domain nonlocal problem and its multi‐domain reformulation, both at the continuous and discrete levels. These results provide the rigorous foundation necessary for the development of efficient solution strategies for nonlocal DD methods.

Capodaglio, Giacomo↗
DOE OSTI2024

HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold

Abstract Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C‐terminus of ICP0 was purified from bacteria and analyzed by X‐ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β‐strands and two α‐helices. Interestingly, two adjacent β‐strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β‐barrel‐like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β‐strands of each dimer, creating a “stacking” of the β‐barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C‐terminal SUMO‐interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV‐1 life cycle.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Domain wall motion across microstructural features in polycrystalline ferroelectric films

This paper describes the effect of microstructural features such as grain boundaries and triple points on the pinning of domain wall motion in perovskite Pb(Zr 0.52 Ti 0.48 )O 3 (PZT) films on polycrystalline SrRuO 3 /SrTiO 3 substrates. Here, spatial variability in the collective domain wall dynamics was assessed using non-linearity mapping via Band Excitation Piezoresponse Force Microscopy (BE-PFM). Collocating the non-linearity maps with triple point locations (as visualized by EBSD) allowed for exploration of the effects that local microstructure (e.g., grain boundary) have on domain wall motion. It was found that the extrinsic behavior varied with both the misorientation angle and the proximity to the grain boundary. The width of influence of individual grain boundaries on the motion of domain walls was a function of the character of the grain boundary; random grain boundaries exhibit deeper minima in α d /d 33,initial and larger widths of influence (up to 905 nm) compared to coincident site lattice (CSL) boundaries (up to 572 nm). Additionally, triple points containing larger numbers of random boundaries exhibited non-Rayleigh behavior to greater distances, suggesting that the triple point provides either a deep potential minimum or a region where domain wall motion is unfavorable.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A parametric approach to identify synergistic domains of process intensification for reactive separation

Process intensification aims to combine multiple tasks within multi-functional units to drastically improve economic, energy or sustainability metrics of a chemical process. Limited work exists to systematically identify the synergistic domains where intensification outperforms its nonintensified counterpart. In this work, we computationally derive the synergistic domains of a reactive separation system. Specifically, we first postulate general models for both intensified and nonintensified systems. We use these models to generate data to train a ReLU-type artifical neural network (ANN). Further, the trained ReLU-NN model is formulated as a multi-parametric mixed-integer linear program (mp-MILP), and the critical regions of this mp-MILP define the synergistic feasible domains of intensification. We have derived these synergistic domains of vapor–liquid equilibrium (VLE)-based reactive separation for several industrial applications. These synergistic domains enable quick screening of properties that favor intensification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Deformation accommodating periodic computational domain for a uniform velocity gradient

Many multiscale methods for granular materials use periodic computational domains to consider particle scale interactions and then calculate the stress to drive the continuum scale calculations. For problems involving large material deformations, the computation domain often needs to be reinitialized because of the distortion, causing the loss of the history information of the system. This work introduces an algorithm to accommodate a large deformation of the material while maintaining the computational domain cuboid to avoid the domain reinitialization during the computation. The algorithm uses a rotating frame of reference, in which the velocity gradient can be represented by an upper triangular matrix. The deformation caused by the upper triangular matrix is treated by the image system implied in the periodicity to maintain the computational domain cuboid. The effect from the rotation of the reference frame is considered using the inertial forces. Finally, simulations of simple and pure shear motions are carried out to illustrate the algorithm.

42 ENGINEERING↗
DOE OSTI2023

Structural and Biophysical Properties of a [4Fe-4S] Ferredoxin-Like Protein from Synechocystis sp. PCC 6803 with a Unique Two Domain Structure

Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron-sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe-2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2x[4Fe-4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 +/- 9 mV and -516 +/- 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe-4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.

cyanobacteria↗
DOE OSTI2023

Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation

SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the “PTP-dead” C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for inhibition of coagulation factor VIII reveals a shared antigenic hotspot on the C1 domain

Hemophilia A arises from dysfunctional or deficient coagulation factor (F)VIII and leads to inefficient fibrin clot formation and uncontrolled bleeding events. The development of antibody inhibitors is a clinical complication in hemophilia A patients receiving FVIII replacement therapy. LE2E9 is an anti-C1 domain inhibitor previously isolated from a mild/moderate hemophilia A patient and disrupts FVIII interactions with von Willebrand factor and FIXa, though the intermolecular contacts that underpin LE2E9-mediated FVIII neutralization are undefined. To determine the structure of the complex between FVIII and LE2E9 and characterize its mechanism of inhibition. FVIII was bound to the antigen binding fragment (Fab) of NB2E9, a recombinant construct of LE2E9, and its structure was determined by cryogenic electron microscopy. Here, this report communicates the 3.46 Å structure of FVIII bound to NB2E9, with its epitope comprising FVIII residues S2040 to Y2043, K2065 to W2070, and R2150 to H2155. Structural analysis reveals that the LE2E9 epitope overlaps with portions of the epitope for 2A9, a murine-derived inhibitor, suggesting that these residues represent a shared antigenic region on the C1 domain between FVIII –/– mice and hemophilia A patients. Furthermore, the FVIII:NB2E9 structure elucidates the orientation of the LE2E9 glycan, illustrating how the glycan sterically blocks interactions between the FVIII C1 domain and the von Willebrand factor D' domain. A putative model of the FVIIIa:FIXa complex suggests potential clashing between the NB2E9 glycan and FIXa light chain. These results describe an antigenic “hotspot” on the FVIII C1 domain and provide a structural basis for engineering FVIII replacement therapeutics with reduced antigenicity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Determining the domain-level reaction-diffusion properties of an actin-binding protein transgelin-2 within cells

Proteins in cells undergo repeated binding to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical binding, it is difficult with conventional approaches to attribute the measured quantities to the nature of specific domains of the proteins. Motivated by the common goal in cell signaling research aimed at identifying the domains responsible for particular intermolecular interactions, here we describe a framework for determining the local physicochemical properties of cellular proteins associated with immobile scaffolds. To validate this new approach, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created, and the difference among them in FRAP response is analyzed. We demonstrate that transgelin-2 in actin stress fibers (SFs) interacts with F-actin via two separate domains, and the chemical properties are determined for the individual domains. Its pure diffusion properties independent of the association to F-actin is also obtained. Our approach will thus be useful, as presented here for transgelin-2, in addressing the signaling mechanism of cellular proteins associated with SFs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Protein Surface Printer for Exploring Protein Domains

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗