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At least 433 records · Page 24

Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state

Abstract AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH ( Tm FtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length Tm FtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.

59 BASIC BIOLOGICAL SCIENCES↗

Frequency domain identification experiment on a large flexible structure

Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. The authors highlight an automated frequency domain system identification methodology recently developed to fill this need. The methodology supports (1) the estimation of system quantities useful for robust control analysis and design, (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment, and (3) the automation of operations to reduce human-in-the-loop requirements. A basic overview of the methodology is presented first, followed by an experimental verification of the approach performed on the JPL/AFAL testbed facility.

Bayard, D. S.↗

Further developments in the controlled growth approach for optimal structural synthesis

It is pointed out that the use of nonlinear programming methods in conjunction with finite element and other discrete analysis techniques have provided a powerful tool in the domain of optimal structural synthesis. The present investigation is concerned with new strategies which comprise an extension to the controlled growth method considered by Hajela and Sobieski-Sobieszczanski (1981). This method proposed an approach wherein the standard nonlinear programming (NLP) methodology of working with a very large number of design variables was replaced by a sequence of smaller optimization cycles, each involving a single 'dominant' variable. The current investigation outlines some new features. Attention is given to a modified cumulative constraint representation which is defined in both the feasible and infeasible domain of the design space. Other new features are related to the evaluation of the 'effectiveness measure' on which the choice of the dominant variable and the linking strategy is based.

Hajela, P.↗

Large-eddy simulation of an atmospheric bore and associated gravity wave effects on wind farm performance in the southern Great Plains

Gravity waves are a common occurrence in the atmosphere, with a variety of generation mechanisms. Their impact on wind farms has only recently gained attention, with most studies focused on wind farm-induced gravity waves. In this study, the interaction between a wind farm and gravity waves generated by an atmospheric bore event is assessed using multiscale large-eddy simulations. The atmospheric bore is created by a thunderstorm downdraft from a nocturnal mesoscale convective system (MCS). The associated gravity waves impact the wind resource and power production at a nearby wind farm during the American Wake Experiment (AWAKEN) in the US southern Great Plains. A two-domain nested setup (Δx=300 and 20 m) is used in the Weather Research and Forecasting (WRF) model, forced with data from the High-Resolution Rapid Refresh model, to capture both the formation of the bore and its interaction with individual wind turbines. The MCS is resolved on the large outer domain, where the structure of the bore and the associated gravity waves are found to be especially sensitive to parameterized microphysics processes. On the finer inner domain, gravity wave interactions with individual wind turbines are resolved; wake dynamics are captured using a generalized actuator disk parameterization in WRF. The gravity waves are found to have a strong effect on the atmosphere above the wind farm; however, the effect of the waves is more nuanced closer to the surface where there is additional turbulence, both ambient and wake-generated. Notably, the gravity waves modulate the mesoscale environment by weakening and dissipating the preexisting low-level jet, which reduces hub-height wind speed and hence the simulated power output, which is confirmed by the observed supervisory control and data acquisition (SCADA) power data. Additionally, the gravity waves induce local wind direction variations correlated with fluctuations in pressure, which lead to fluctuations in the simulated power output as various turbines within the farm are subjected to waking from nearby turbines.

17 WIND ENERGY↗

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

Biochemistry & Molecular Biology↗

IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

Significance Polycomb Repressive Complex 2 (PRC2) methylates histones to regulate multicellular development, maintenance of stem cell identity, X-chromosome inactivation, and other important processes. Given these essential roles, there is significant interest in identifying components that function with PRC2 to establish and maintain transcriptionally repressive heterochromatin. Here we document an unexpected new role for a well-studied and conserved chromatin remodeling factor, ISWI. We found that the Neurospora ISWI homolog is required for normal facultative heterochromatin structure and gene repression at PRC2 target regions, and we defined requirements for ATP-dependent catalytic activity and accessory regulatory proteins. These findings provide mechanistic insights into the formation and function of facultative heterochromatin in a model eukaryote.

Kamei, Masayuki↗

A numerical-homogenization based phase-field fracture modeling of linear elastic heterogeneous porous media

Most porous media, such as geomaterials and biomaterials are highly heterogeneous in nature, and they contain large variations of microscopic pore structures, such as pore sizes, pore distribution, and pore shapes. The oscillation of microscopic structures is a substantial challenge in theoretical characterization and is usually ignored in continuous modeling. However, mechanical behavior of porous media such as deformation and failure, are essentially impacted by the microscopic heterogeneity which needs to be considered in modeling a porous media. Here, this research proposes a numerical modeling framework with a capability to investigate the effect of microscopic heterogeneity on the macroscopic fracture behavior in porous media by using a numerical homogenization technique, combined with the phase-field fracture modeling method. This numerical modeling strategy computes a homogenized elasticity tensor based on microscopic heterogeneous pore structures heterogenous porous domain by solving boundary value problems at microscopic domain. The strain energy and subsequent propagation of macroscopic fractures will be updated using homogenized stiffness information. Using this numerical scheme, the microscopic pore structure’s impact on the fracture behavior through the homogenized elastic tensor will be taken into account. This multiscale technique is benchmarked against classical problems. Finally, the results highlight the importance of the underlying pore structure and reveal that both fracture strength and propagation path can be influenced by the microscopic heterogeneity.

36 MATERIALS SCIENCE↗

X-ray Nanoimaging of Crystal Defects in Single Grains of Solid-State Electrolyte Li 7–3x Al x La 3 Zr 2 O 12

All-solid-state lithium batteries promise significant improvements in energy density and safety over traditional liquid electrolyte batteries. The Al-doped Li 7 La 3 Zr 2 O 12 (LLZO) solid-state electrolyte shows excellent potential given its high ionic conductivity and good thermal, chemical, and electrochemical stability. Nevertheless, further improvements on electrochemical and mechanical properties of LLZO call for an in-depth understanding of its local microstructure. Here, we employ Bragg coherent diffractive imaging to investigate the atomic displacements inside single grains of LLZO with various Al-doping concentrations, resulting in cubic, tetragonal, and cubic-tetragonal mixed structures. We observe coexisting domains of different crystallographic orientations in the tetragonal structure. We further show that Al doping leads to crystal defects such as dislocations and phase boundaries in the mixed- and cubic-phase grain. This study addresses the effect of Al doping on the nanoscale structure within individual grains of LLZO, which is informative for the future development of solid-state batteries.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Strain-Induced Atomic-Scale Building Blocks for Ferromagnetism in Epitaxial LaCoO 3

The origin of strain-induced ferromagnetism, which is robust regardless of the type and degree of strain in LaCoO 3 (LCO) thin films, is enigmatic despite intensive research efforts over the past decade. Here, by combining scanning transmission electron microscopy with ab initio density functional theory plus U calculations, we report that the ferromagnetism does not emerge directly from the strain itself but rather from the creation of compressed structural units within ferroelastically formed twin-wall domains. Here, the compressed structural units are magnetically active with the rocksalt-type high-spin/low-spin order. Our study highlights that the ferroelastic nature of ferromagnetic structural units is important for understanding the intriguing ferromagnetic properties in LCO thin films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Piezoelectric domain walls in van der Waals antiferroelectric CuInP2Se6

Polar van der Waals chalcogenophosphates exhibit unique properties, such as negative electrostriction and multi-well ferrielectricity, and enable combining dielectric and 2D electronic materials. Using low temperature piezoresponse force microscopy, we revealed coexistence of piezoelectric and non-piezoelectric phases in CuInP2Se6, forming unusual domain walls with enhanced piezoelectric response. From systematic imaging experiments we have inferred the formation of a partially polarized antiferroelectric state, with inclusions of structurally distinct ferrielectric domains enclosed by the corresponding phase boundaries. The assignment is strongly supported by optical spectroscopies and density-functional-theory calculations. Enhanced piezoresponse at the ferrielectric/antiferroelectric phase boundary and the ability to manipulate this entity with electric field on the nanoscale expand the existing phenomenology of functional domain walls. At the same time, phase-coexistence in chalcogenophosphates may lead to rational strategies for incorporation of ferroic functionality into van der Waals heterostructures, with stronger resilience toward detrimental size-effects.

36 MATERIALS SCIENCE↗

Giant piezoelectricity in oxide thin films with nanopillar structure

High-performance piezoelectric materials are critical components for electromechanical sensors and actuators. For more than 60 years, the main strategy for obtaining large piezoelectric response has been to construct multiphase boundaries, where nanoscale domains with local structural and polar heterogeneity are formed, by tuning complex chemical compositions. We used a different strategy to emulate such local heterogeneity by forming nanopillar regions in perovskite oxide thin films. We obtained a giant effective piezoelectric coefficient d 33 , f * of ~1098 picometers per volt with a high Curie temperature of ~450°C. Our lead-free composition of sodium-deficient sodium niobate contains only three elements (Na, Nb, and O). The formation of local heterogeneity with nanopillars in the perovskite structure could be the basis for a general approach to designing and optimizing various functional materials.

Science & Technology - Other Topics↗

Direct visualization and control of antiferromagnetic domains and spin reorientation in a parent cuprate

Here, we report magnetic optical second-harmonic generation (SHG) polarimetry and imaging on Sr 2 Cu 3 O 4 Cl 2 , which allows direct visualization of the mesoscopic antiferromagnetic (AFM) structure of a parent cuprate. Temperature- and magnetic-field-dependent SHG reveals large domains with 90° relative orientations that are stabilized by a combination of uniaxial magnetic anisotropy and the Earth's magnetic field. Below a temperature T R ~ 97 K, we observe an unusual 90° spin reorientation transition, possibly driven by competing magnetic anisotropies of the two copper sublattices, which swaps the AFM domain states while preserving the domain structure. This allows deterministic switching of the AFM states by thermal or laser heating. Near T R , the domain walls become exceptionally responsive to an applied magnetic field, with the Earth's field sufficient to completely expel them from the crystal. Our findings unlock opportunities to study the mesoscopic AFM behavior of parent cuprates and explore their potential for AFM technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Asymmetric Character of the Ferroelectric Phase Transition and Charged Domain Walls in a Hybrid Improper Ferroelectric

Abstract In improper ferroelectrics, the spontaneous ordering is typically driven by a structural distortion or a magnetic spin alignment. The induced electric polarization is only a secondary effect. This dependence is a rich source for unusual phenomena and ferroelectric domain configurations for proper, polarization‐driven ferroelectrics. This study focuses on the polar domain structure and the hysteretic behavior at the ferroelectric phase transition in Ca 3 Mn 1.9 Ti 0.1 O 7 as a representative of the recently discovered hybrid improper ferroelectric class of multiferroics. Combining optical second harmonic generation and Raman spectroscopy gives access to the spontaneous structural distortion and the resulting improper electric polarization. This study shows that hybrid improper ferroelectrics contrast proper and improper ferroelectrics in several ways. Most intriguingly, adjacent ferroelectric domains favor head‐to‐head and tail‐to‐tail domain walls over charge‐neutral configurations. Furthermore, the phase transition occurs in an asymmetric fashion. The regime of phase coexistence of the nonpolar and polar phases shows a clear and abrupt upper temperature limit. In contrast, the coexistence toward low temperatures is best described as a fade‐out process, where 100‐nm‐sized islands of the nonpolar phase expand deep into the polar phase.

36 MATERIALS SCIENCE↗

Cesium exhibits different mesoscale segregation and ion pairing than lithium, sodium, or potassium in concentrated alkaline aqueous nitrite solutions

Understanding ion pairing in concentrated alkaline electrolytes facilitates the prediction and control of chemical processes in nuclear waste. While sodium is the dominant alkali metal in such systems, cesium often exhibits distinct bulk behavior relative to lighter alkali cations. Aqueous mixtures of cesium hydroxide and sodium nitrite were compared to alkali hydroxide analogs using small-angle x-ray scattering, revealing that cesium disrupts the sodium nitrite electrolyte structure, forming cesium-rich domains. This mesoscale segregation contrasts with the near-ideal mixing observed in other mixed hydroxide–nitrite systems. Raman spectroscopy indicates cesium–nitrite ion pairing, evidenced by vibrational shifts distinct from those associated with sodium. Multinuclear magnetic resonance spectroscopy further supports cesium–nitrite and cesium–hydroxide association, revealing a distinct local environment for nitrite in cesium-containing solutions. Together, these findings show that cesium promotes a unique solution structure dominated by specific ion pairing within segregated domains. This structural organization may influence radical generation pathways in high-ionic-strength alkaline media relevant to nuclear waste processing and management.

Nienhuis, Emily T. [Pacific Northwest National Lab↗

ISAAC (integrated Structural Analysis and Control) via Continuum Modeling and Distributed Frequency Domain Design Techniques

A methodology is proposed for the integrated design of structures and their controls. The integration of design is accomplished through simultaneous selection, via optimization, of designer-specified parameters governing the structure and its controller. The cost function is chosen to address the primary structural and control goals. Inequality constraints are added to insure that additional design requirements are met. The methodology is illustrated through development of an example involving a cantilever beam. A distributed transfer function is derived from the Bernoulli-Euler beam equation. A controller parameterization is then chosen, and performance requirements specified. A controller is then obtained via optimization, which is shown to give good performance.

Gustafson, C. L.↗

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins

Abstract RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron–electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

Biochemistry & Molecular Biology↗

Directional effects of antiferromagnetic ordering on the electronic structure in NdSb

The recent discovery of unconventional surface-state pairs, which give rise to Fermi arcs and spin textures, in antiferromagnetically ordered NdBi raised the interest in rare-earth monopnictides. Several scenarios of antiferromagnetic (AFM) order have been suggested to explain the origin of these states with some of them being consistent with the presence of nontrivial topologies. Here, in this paper, we use angle-resolved photoemission spectroscopy (ARPES) and density-functional-theory (DFT) calculations to investigate the electronic structure of NdSb. We found the presence of distinct domains that have different electronic structures at the surface. These domains correspond to different orientations of magnetic moments in the AFM state with respect to the surface. We demonstrated remarkable agreement between DFT calculations and ARPES that capture all essential changes in the band structure caused by the transition to a magnetically ordered state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Joint Matrix Completion and Compressed Sensing for State Estimation in Low-observable Distribution System

Limited measurement availability at the distribution grid presents challenges for state estimation and situational awareness. This paper combines the advantages of two sparsity-based state estimation approaches (matrix completion and compressive sensing) that have been proposed recently to address the challenge of unobservability. The proposed approach exploits both the low rank structure and a suitable transform domain representation to leverage the correlation structure of the spatio-temporal data matrix while incorporating the powerflow constraints of the distribution grid. Simulations are carried out on three phase unbalanced IEEE 37 test system to verify the effectiveness of the proposed approach. The performance results reveal - (1) the superiority over traditional matrix completion and (2) very low state estimation errors for high compression ratios representing very low observability.

Dahale, Shweta↗