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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant

Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The exo-β- N -acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases

Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that catalyze an endo-lytic cleavage of peptidoglycan; i.e., they hydrolyze the β-1,4-glycosidic bonds connecting N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). In contrast, little is known about exo-β-N-acetylmuramidases, which catalyze an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We now report that ybbC of B. subtilis, renamed namZ, encodes the reported exo-β-N-acetylmuramidase. A ΔnamZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover and recycling. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. A structure model of NamZ, built on the basis of two crystal structures of putative orthologs from Bacteroides fragilis, revealed a two-domain structure including a Rossmann-fold-like domain that constitutes a unique glycosidase fold. Thus, NamZ, a member of the DUF1343 protein family of unknown function, is now classified as the founding member of a new family of glycosidases (CAZy GH171). NamZ-like peptidoglycan hexosaminidases are mainly present in the phylum Bacteroidetes and less frequently found in individual genomes within Firmicutes (Bacilli, Clostridia), Actinobacteria, and γ-proteobacteria.

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

Magnetochiral tunneling in paramagnetic Co 1/3 NbS 2

Electric currents have the intriguing ability to induce magnetization in nonmagnetic crystals with sufficiently low crystallographic symmetry. Some associated phenomena include the non-linear anomalous Hall effect in polar crystals and the nonreciprocal directional dichroism in chiral crystals when magnetic fields are applied. In this work, we demonstrate that the same underlying physics is also manifested in the electronic tunneling process between the surface of a nonmagnetic chiral material and a magnetized scanning probe. In the paramagnetic but chiral metallic compound Co 1/3 NbS 2 , the magnetization induced by the tunneling current is shown to become detectable by its coupling to the magnetization of the tip itself. This results in a contrast across different chiral domains, achieving atomic-scale spatial resolution of structural chirality. To support the proposed mechanism, we used first-principles theory to compute the chirality-dependent current-induced magnetization and Berry curvature in the bulk of the material. Our demonstration of this magnetochiral tunneling effect opens up an avenue for investigating atomic-scale variations in the local crystallographic symmetry and electronic structure across the structural domain boundaries of low-symmetry nonmagnetic crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural Phase Separation and Enhanced Superconductivity in La 1.875 Ba 0.125 CuO 4 Under Uniaxial Strain

Strain engineering has attracted significant attention in recent years due to its capability in tuning lattice and electronic structures of quantum materials. Using moderate uniaxial compressive strain, structural phase separation is induced in the low-temperature phase of x = 1/8 La 2-x Ba x CuO 4 (LBCO) single crystals. These structures are low temperature tetragonal (LTT), low temperature less orthorhombic (LTLO), and a plastically deformed nano-domain structure (PDNS), comprised of few-nanometer-sized orthorhombic domains within an amorphous matrix. These three structures exhibit distinct superconducting behaviors. The volume fraction of the LTT structure is suppressed with increasing strain, while its superconducting transition temperature increases and broadens. The LTLO structure exhibits a sharp superconducting transition above 32 K, which increases up to ≈ 36 K at maximum strain. The PDNS phase exhibits a very broad superconducting transition and persists even after removing the strain. This study illustrates the sensitivity of superconductivity to the structure of the LBCO sample near its stripe instability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Enhanced domain dynamics in alternating current poled rhombohedral Pb(Mg 1/3 Nb 2/3 )O 3 –PbTiO 3 single crystals

Abstract The understanding of domain dynamics in ferroelectric materials is crucial for optimizing their performance in piezoelectric and electro‐optic applications. Although previous studies have focused on static domain structures and macroscopic characteristics, the time‐resolved approach of domains remains largely unexplored. In this study, we compare the dynamic responses of direct current (DC) and alternating current (AC) poled [001]‐oriented rhombohedral Pb(Mg 1/3 Nb 2/3 )O 3 –PbTiO 3 (PMN–PT) single crystals using X‐ray photon correlation spectroscopy (XPCS) during the application of external electric fields. Our results demonstrate that the AC‐poled sample exhibit enhanced reconfiguration of domain variants in response to driving fields compared to the DC‐poled counterpart, as evidenced by accelerated correlation decay and faster relaxation time. This phenomenon is attributed to enhanced reversible domain wall motion achieved through AC poling, which facilitates field‐induced domain realignment. These findings provide insight into the relationship between dynamics and macroscopic properties in relaxor‐PT single crystals for high‐performance applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗
DOE OSTI2025

Quantum confining excitons with an electrostatic moiré superlattice

Quantum confining excitons has been a persistent challenge in the pursuit of strong exciton interactions and quantum light generation. Unlike electrons, which can be readily controlled via electric fields, imposing strong nanoscale potentials on excitons to enable quantum confinement has proven challenging. In this study, we utilize piezoelectric force microscopy to image the domain structures of twisted hexagonal boron nitride (h – BN), revealing evidence of strong in-plane electric fields at the domain boundaries. By placing a monolayer MoSe 2 only one to two nanometers away from the twisted h – BN interface, we observe energy splitting of neutral excitons and Fermi polarons by several millielectronvolts at the moiré domain boundaries. By directly correlating local structural and optical properties, we attribute such observations to excitons confined in a nanoscale one-dimensional electrostatic potential created by the strong in-plane electric fields at the moiré domain boundaries. Intriguingly, this 1D quantum confinement results in pronounced polarization anisotropy in the excitons’ reflection and emission, persistent to temperatures as high as ~80 Kelvins. Furthermore, these findings open new avenues for exploring and controlling strongly interacting excitons for classical and quantum optoelectronics.

2-dimensional systems↗
DOE OSTI2021

A coupled discontinuous Galerkin-Finite Volume framework for solving gas dynamics over embedded geometries

Herein, we present a computational framework for solving the equations of inviscid gas dynamics using structured grids with embedded geometries. The novelty of the proposed approach is the use of high-order discontinuous Galerkin (dG) schemes and a shock-capturing Finite Volume (FV) scheme coupled via an hp adaptive mesh refinement (hp-AMR) strategy that offers high-order accurate resolution of the embedded geometries. The hp-AMR strategy is based on a multi-level block-structured domain partition in which each level is represented by block-structured Cartesian grids and the embedded geometry is represented implicitly by a level set function. The intersection of the embedded geometry with the grids produces the implicitly-defined mesh that consists of a collection of regular rectangular cells plus a relatively small number of irregular curved elements in the vicinity of the embedded boundaries. High-order quadrature rules for implicitly-defined domains enable high-order accuracy resolution of the curved elements with a cell-merging strategy to address the small-cell problem. The hp-AMR algorithm treats the system with a second-order finite volume scheme at the finest level to dynamically track the evolution of solution discontinuities while using dG schemes at coarser levels to provide high-order accuracy in smooth regions of the flow. On the dG levels, the methodology supports different orders of basis functions on different levels. The space-discretized governing equations are then advanced explicitly in time using high-order Runge-Kutta algorithms. Numerical tests are presented for two-dimensional and three-dimensional problems involving an ideal gas. The results are compared with both analytical solutions and experimental observations and demonstrate that the framework provides high-order accuracy for smooth flows and accurately captures solution discontinuities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Probing Metastable Domain Dynamics via Automated Experimentation in Piezoresponse Force Microscopy

The dynamics of complex topological defects in ferroelectric materials is explored using automated experimentation in piezoresponse force microscopy. Specifically, a complex trigger system (i.e., “FerroBot”) is employed to study metastable domain-wall dynamics in Pb 0.6 Sr 0.4 TiO 3 thin films. Several regimes of superdomain wall dynamics have been identified, including smooth domain-wall motion and significant reconfiguration of the domain structures. We have further demonstrated that microscopic mechanisms of the domain-wall dynamics can be identified; i.e., domain-wall bending can be separated from irreversible domain reconfiguration regimes. In conjunction, phase-field modeling was used to corroborate the observed mechanisms. As such, the observed superdomain dynamics can provide a model system for classical ferroelectric dynamics, much like how colloidal crystals provide a model system for atomic and molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Unusual dynamic susceptibility arising from soft ferromagnetic domains in MnBi 8 Te 13 and Sb-doped MnBi 2n Te 3n+1 (n = 2, 3)

MnBi$_{2n}$Te$_{3n+1}$ (MBT) is the first intrinsic magnetic topological insulator and is promising to host emergent phenomena such as quantum anomalous Hall effect. They can be made ferromagnetic by having n ≥ 4 or with Sb doping. In this work, we studied the magnetic dynamics in a few selected ferromagnetic (FM) MBT compounds, including MnBi 8 Te 13 and Sb doped MnBi$_{2n}$Te$_{3n+1}$ ($n = 2, 3)$ using AC susceptibility and magneto-optical imaging. Slow relaxation behavior is observed in all three compounds, suggesting its universality among FM MBT. We attribute the origin of the relaxation behavior to the irreversible domain movements since they only appear below the saturation fields when ferromagnetic domains form. The very soft ferromagnetic domain nature is revealed by the low-field fine-structured domains and high-field sea-urchin-shaped remanent-state domains imaged via our magneto-optical measurements. Finally, we ascribe the rare 'double-peak' behavior observed in the AC susceptibility under small DC bias fields to the very soft ferromagnetic domain formations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Phase-field-guided design of record-high piezoelectricity and discovery of simultaneous high light transparency and high piezoelectricity in relaxor ferroelectrics

Here, the phase-field method has been extensively applied to predicting the domain structures and their responses to external fields and understanding experimentally observed domain states under different electromechanical conditions in ferroelectric heterostructures. This article highlights the successful examples of phase-field applications in guiding the design of relaxor ferroelectric ceramics and crystals with record-high piezoelectricity and the discovery of simultaneous high light transparency and piezoelectricity of relaxor ferroelectric crystals for a wide range of biomedical, robotics, and optoelectronics applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Adaptive methods of generating complex light arrays

Structured light arrays of various shapes have been a cornerstone in optical science, driven by the complexities of precise and adaptable generation. This study introduces an approach using a spatial light modulator (SLM) as a generator for these arrays. By projecting a holographic mask onto the SLM, it functions simultaneously as an optical convolution device, focusing mechanism, and structured light beam mask. Our approach offers unmatched versatility, allowing for the experimental fabrication of traditional beam arrays like azimuthal Laguerre–Gaussian (LG), Bessel–Gaussian (BG), and Hermite–Gauss (HG) in the far-field. Notably, it has enabled a method of generating Ince–Gauss (IG) and LG radial mode beam arrays using a convolution solution. Our system provides exceptional control over array periodicity and intensity distribution, bypassing the Talbot self-imaging phenomenon seen in traditional setups. We provide an in-depth theoretical discussion, supported by empirical evidence, of our far-field results. This method has vast potential for applications in optical communication, data processing, and multi-particle manipulation. It paves the way for rapid generation of structured light with high spatial frequencies and complex shapes, promising transformative advances in these domains.

Optics↗
DOE OSTI2021

Effect of correlated oxide electrodes on disorder pinning and thermal roughening of ferroelectric domain walls in epitaxial PbZr 0.2 Ti 0.8 O 3 thin films

We report the competing effects of disorder pinning and thermal roughening on ferroelectric domain walls as a function of temperature in epitaxial PbZr 0.2 Ti 0.8 O 3 thin films deposited on (001) SrTiO 3 substrates buffered by three types of correlated oxide electrodes, La 0.67 Sr 0.33 MnO 3 , LaNiO 3 , and SrIrO 3 . Piezo-response force microscopy studies show that the 50 nm PbZr 0.2 Ti 0.8 O 3 films are uniformly polarized in the as-grown states, with the patterned domain structures persisting above 700 °C. For all three types of films, the domain wall roughness is dominated by 2D random bond disorder at room temperature, and transitions to 1D thermal roughening upon heating. The roughness exponent ζ increases progressively from 0.3 to 0.5 within a temperature window that depends on the bottom conducting oxide type, from which we extracted the distribution of disorder pinning energy. Lastly, we discuss the possible origins of the disorder pinning and the effect of the correlated oxide electrodes on the energy landscape of DW motion.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Domain fluctuations in a ferroelectric low-strain BaTiO 3 thin film

In this work, a ferroelectric BaTiO 3 thin film grown on a NdScO 3 substrate was studied using x-ray photon correlation spectroscopy (XPCS) to characterize thermal fluctuations near the a/b to a/c domain structure transformation present in this low-strain material, which is absent in the bulk. XPCS studies provide a direct comparison of the role of domain fluctuations in first- and second-order phase transformations. The a/b to a/c domain transformation is accompanied by a decrease in fluctuation timescales, and an increase in intensity and correlation length. Surprisingly, domain fluctuations are observed up to 25 °C above the transformation, concomitant with the growth of a/c domains and coexistence of both domain types. After a small window of stability, as the Curie temperature is approached, a/c domain fluctuations are observed, albeit slower, potentially due to the structural transformation associated with the ferroelectric to paraelectric transformation. The observed time evolution and reconfiguration of domain patterns highlight the role played by phase coexistence and elastic boundary conditions in altering fluctuation timescales in ferroelectric thin films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Controlling quantum phases of electrons and excitons in moiré superlattices

Moiré lattices formed in twisted and lattice-mismatched van der Waals heterostructures have emerged as a platform to engineer the novel electronic and excitonic states at the nanoscale. This Perspective reviews the materials science of moiré heterostructures with a focus on the structural properties of the interface and its structural–property relationships. We first review the studies of the atomic relaxation and domain structures in moiré superlattices and how these structural studies provide critical insights into understanding the behaviors of quantum-confined electrons and excitons. We discuss the general frameworks to manipulate moiré structures and how such control can be harnessed for engineering new phases of matter and simulating various quantum phenomena. Lastly, we discuss routes toward large-scale moiré heterostructures and give an outlook on their applications in quantum electronics and optoelectronics. Special emphasis will be placed on the challenges and opportunities of the reliable fabrication and dynamical manipulation of moiré heterostructures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗