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At least 1,081 records · Page 60

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗

Optical high-order harmonic generation as a structural characterization tool

Structural characterization is essential to material engineering, but few tools can detect structural properties in the time domain. High harmonic generation (HHG) emerges as a new frontier that touches the heart of condensed-matter physics from the symmetry to quantum geometrical nature of electrons, but its capability in structural characterization has not been materialized. Here, we establish a crucial connection between the symmetry of a material and the helicity of light. We employ monolayer MoS 2 as an example. In this work, we show that a linearly polarized laser pulse used in experiments is not ideal for structural characterization because it only generates in-plane anisotropy. It is the circularly polarized laser field that is capable of producing four distinctive HHG signals from the four phases of MoS 2 . This finally links the laser helicity to the crystal structure. The results are generic and are not affected by the Berry curvature, the interband or intraband contribution. Our study unleashes the power of HHG as a structural characterization tool for technologically important materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quasiparticle conductance in spin valve Josephson structures

We study the quasiparticle current in clean ferromagnetic Josephson structures of the form $S_1/F_1/N/F_2/S_2$, where $\textit{S, F,}$ and $\textit{N}$ denote superconducting, ferromagnetic, or normal layers, respectively. Our focus is on the structure of the conductance $\textit{G}$ as a function of bias $\textit{V$, emphasizing the subgap region. We use a fully self-consistent numerical method, coupled to a transfer matrix procedure to extract $\textit{G(V)}$. We choose material parameters appropriate to experimentally realized Co Cu Nb structures. In this work, we find a resonance peak structure as a function of the intermediate layer thickness and of the misalignment angle $\phi$ between $\textit{F}$ layers. To understand this resonance structure, we develop an approximate analytic method. For experimentally relevant thicknesses, the conductance has multiple subgap peaks, which oscillate in position between low and critical bias positions. These oscillations occur in both $\phi$ and the layer thicknesses. We compare our results with those obtained for the spin valve structures ($F_1/N/F_2/S_2$) and discuss the implications of our results for the fabrication of spin Josephson devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Pressure tuning of structural and magnetic transitions in EuAg 4 As 2

We report temperature-dependent measurements of ambient-pressure specific heat, magnetic susceptibility, anisotropic resistivity, and thermal expansion as well as in-plane resistivity under pressure up to 20.8 kbar on single crystals of EuAg 4 As 2 . Based on thermal expansion and in-plane electrical transport measurements at ambient pressure this compound has two, first-order, structural transitions in the 80–120 K temperature range. Ambient-pressure specific heat, magnetization, and thermal expansion measurements show a cascade of up to seven transitions between 8 and 16 K associated with the ordering of the $Eu^{2+}$ moments. In-plane electrical transport is able to detect the more prominent of these transitions, at 15.5, 9.9, and 8.7 K, as well as a weak feature at 11.8 K at ambient pressure. Pressure-dependent electrical transport data show that the magnetic transitions shift to higher temperatures under pressure, as does the upper structural transition, whereas the lower structural transition is suppressed and ultimately vanishes. A jump in resistivity, associated with the upper structural transition, decreases under pressure with an extrapolated disappearance (or a change of sign) by 30–35 kbar. In the 10–15 kbar range a kink in the pressure dependency of the upper structural transition temperature as well as the high- and low-temperature in-plane resistivities suggests that a change in the electronic structure may occur in this pressure range. The results are compared with the literature data for EuAg 4 As 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High critical field superconductivity at ambient pressure in MoB 2 stabilized in the P6/mmm structure via Nb substitution

Recently it was discovered that, under elevated pressures, MoB 2 exhibits superconductivity at a critical temperature T c as high as 32 K. The superconductivity appears to develop following a pressure-induced structural transition from the ambient pressure $\text{R}\bar{3}$⁢m structure to an MgB 2 -like P6/mmm structure. This suggests that remarkably high T c values among diborides are not restricted to MgB 2 as previously appeared to be the case, and that similarly high T c values may occur in other diborides if they can be coerced into the MgB 2 structure. In this paper, we show that density functional theory calculations indicate that phonon free energy stabilizes the P6/mmm structure over the $\text{R}\bar{3}$⁢m at high temperatures across the Nb 1–x ⁢Mo x B 2 series. X-ray diffraction confirms that the synthesized Nb-substituted MoB 2 adopts the MgB 2 crystal structure. Finally, high magnetic field electrical resistivity measurements and specific heat measurements demonstrate that Nb x ⁢Mo 1–x⁢ B 2 exhibits superconductivity with T c as high as 8 K and critical fields approaching 6 T.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ferroelectric switching pathways and domain structure of SrBi 2 ⁢(Ta,Nb) 2 ⁢O 9 from first principles

Several families of layered perovskite oxide ferroelectrics exhibit a coupling between polarization and structural order parameters, such as octahedral rotation distortions. This coupling provides opportunities for novel electric field-based manipulation of material properties, and it also stabilizes complex domain patterns and domain-wall vortices. Among layered perovskites with such coupled orders, the Aurivillius-phase oxides SrBi 2 ⁢B 2 ⁢O 9 (B = Ta,Nb) are well-known for their excellent room-temperature ferroelectric performance. This work combines group theoretic analysis with density functional theory calculations to examine the ferroelectric switching processes of SrBi2⁢B2⁢O9. Low-energy two-step ferroelectric switching paths are identified, with polarization reversal facilitated by structural order-parameter rotations. Analysis of the domain structure reveals how the relative energetics of the coupled order parameters translates into a network of several distinct domain-wall types linked by domain-wall vortex structures. Comparisons are made between the ferroelectric switching and domain structure of SrBi 2 ⁢B 2 ⁢O 9 and those of the layered n = 2 Ruddlesden-Popper hybrid improper ferroelectrics. The results provide insight into how ferroelectric properties may be optimized by engineering the complex crystal structures of Aurivillius-phase oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nanoscale structural correlations in a model cuprate superconductor

Understanding the extent and role of inhomogeneity is a pivotal challenge in the physics of cuprate superconductors. While it is known that structural and electronic inhomogeneity is prevalent in the cuprates, it has proven difficult to disentangle compound-specific features from universally relevant effects. Here, in this study, we combine advanced neutron and x-ray diffuse scattering with numerical modeling to obtain insight into bulk structural correlations in HgBa 2 ⁢ CuO 4+δ . This cuprate exhibits a high optimal transition temperature of nearly 100 K, pristine charge-transport behavior, and a simple average crystal structure without long-range structural instabilities, and is therefore uniquely suited for investigations of intrinsic inhomogeneity. We uncover diffuse reciprocal-space patterns that correspond to prominent nanoscale correlations of atomic displacements perpendicular to the CuO 2 planes. The real-space nature of the correlations is revealed through three-dimensional pair distribution function analysis and complementary numerical refinement. We find that relative displacements of ionic and CuO 2 layers play a crucial role, and that the structural inhomogeneity is not directly caused by the presence of conventional point defects. The observed correlations are therefore intrinsic to HgBa 2 ⁢ CuO 4+δ , and thus likely important for the physics of cuprates more broadly. It is possible that the structural correlations are closely related to the unusual superconducting fluctuations and Mott-localization in these complex oxides. As advances in scattering techniques yield increasingly comprehensive data, the experimental and analysis tools developed here for large volumes of diffuse scattering data can be expected to aid future investigations of a wide range of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic structure, self-doping, and superconducting instability in the alternating single-layer trilayer stacking nickelates La 3 ⁢Ni 2 ⁢O 7

Motivated by the recently proposed alternating single-layer trilayer stacking structure for the nickelate La 3 ⁢Ni 2 ⁢O 7 , we comprehensively study this system using ab initio and random-phase approximation techniques. Here, our analysis unveils similarities between this novel La 3⁢ Ni 2 ⁢O 7 structure and other Ruddlesden-Popper nickelate superconductors, such as a similar charge-transfer gap value and orbital-selective behavior of the eg orbitals. Pressure primarily increases the bandwidths of the Ni e g bands, suggesting an enhancement of the itinerant properties of those e g states. By changing the cell volume ratio V/V 0 from 0.9 to 1.10, we found that the bilayer structure in La 3 ⁢Ni 2 ⁢O 7 always has lower energy than the single-layer trilayer stacking La 3 ⁢Ni 2 ⁢O 7 . In addition, we observe a “self-doping” effect (compared to the average 1.5 electrons per eg orbital per site of the entire structure) from the trilayer to the single-layer sublattices and this effect will be enhanced by overall electron doping. Moreover, we find a leading d x 2 -y 2 -wave pairing state that is restricted to the single layer. Because the effective coupling between the single layers is very weak, due to the nonsuperconducting trilayer in-between, this suggests that the superconducting transition temperature T c in this structure should be much lower than in the bilayer structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Examining the EMC effect using the ${F}_{2}^{n}$ neutron structure function

The persistently mysterious deviations from unity of the ratio of nuclear target structure functions to those of deuterium as measured in deep inelastic scattering (often termed the “EMC effect”) have become the canonical observable for studies of nuclear medium modifications to free nucleon structure in the valence regime. The structure function of the free proton is well known from numerous experiments spanning decades. The free neutron structure function, however, has remained difficult to access. Recently it has been extracted in a systematic study of the global data within a parton distribution function extraction framework and is available from the CTEQ–Jefferson Lab (CJ) Collaboration. Here, we leverage the latter to introduce a new method to study the EMC effect in nuclei by reexamining existing data in light of the the magnitude of the medium modifications to the free neutron and proton structure functions independently. From the extraction of the free neutron from world data, it is possible to examine the nuclear effects in deuterium and their contribution to our interpretation of the EMC effect. In this study, we observe that the ratio of the deuteron to the sum of the free neutron and proton structure functions has some x B and Q 2 dependencies that impact the magnitude of the EMC effect as typically observed. Specifically, different EMC slopes are obtained when data from different x B and Q 2 values are utilized. Furthermore, while a linear correlation persists between the EMC and short range correlation effects, the slope is modified when deuteron nuclear effects are removed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

New Structures in the J / ψ J / ψ Mass Spectrum in Proton-Proton Collisions at s = 13 TeV

A search is reported for near-threshold structures in the J / ψ J / ψ invariant mass spectrum produced in proton-proton collisions at s = 13 TeV from data collected by the CMS experiment, corresponding to an integrated luminosity of 135 fb − 1 . Three structures are found, and a model with quantum interference among these structures provides a good description of the data. A new structure is observed with a local significance above 5 standard deviations at a mass of 6638 − 38 + 43 ( stat ) − 31 + 16 ( syst ) MeV . Another structure with even higher significance is found at a mass of 6847 − 28 + 44 ( stat ) − 20 + 48 ( syst ) MeV , which is consistent with the X ( 6900 ) resonance reported by the LHCb experiment and confirmed by the ATLAS experiment. Evidence for another new structure, with a local significance of 4.7 standard deviations, is found at a mass of 7134 − 25 + 48 ( stat ) − 15 + 41 ( syst ) MeV . Results are also reported for a model without interference, which does not fit the data as well and shows mass shifts up to 150 MeV relative to the model with interference. © 2024 CERN, for the CMS Collaboration 2024 CERN

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Structure and migration of heavily irradiated grain boundaries and dislocations in Ni in the athermal limit

The microstructural evolution at and near preexisting grain boundaries (GBs) and dislocations in materials under high radiation doses is still poorly understood. In this work, we use the creation relaxation algorithm (CRA) developed for atomistic modeling of high-dose irradiation in bulk materials to probe the athermal limit of saturation of GB and dislocation core regions under irradiation in fcc Ni. We find that, upon continuously subjecting a single dislocation or GB to Frenkel pair creation in the athermal limit, a local steady-state disordered defect structure is reached with excess properties that fluctuate around constant values. Case studies are given for a straight screw dislocation which elongates into a helix under irradiation and several types of low- and high-angle GBs, which exhibit coupled responses such as absorption of extrinsic dislocations, roughening, and migration. A positive correlation is found between the initial GB energy and the local steady-state GB energy under irradiation across a wide variety of GB types. Metastable GB structures with similar density in the defect core region but different initial configurations are found to converge to the same limiting structure under CRA. The mechanical responses of pristine and irradiated dislocations and GB structures are compared under an applied shear stress. Irradiated screw and edge dislocations are found to exhibit a hardening response, migrating at larger flow stresses than their pristine counterparts. Mobile GBs are found to exhibit softening or hardening responses depending on GB character. Although some GBs recover their initial pristine structures upon migration outside of the radiation zone, many GBs sustain different flow stresses corresponding to altered mobile core structures.

36 MATERIALS SCIENCE↗

Structural and electronic changes in L⁢i 2 ⁢Ru⁢O 3 induced by lithium intercalation

Despite extensive research on oxide battery cathodes that transcend classical cationic redox activity, the detailed interplay between structural transformations and electronic redox processes remains insufficiently understood. We report a detailed study of the sequential structural and electronic changes in Li 2 RuO 3 upon lithium intercalation, characterized by powder x-ray and neutron diffraction alongside Ru and O K-edge x-ray absorption spectroscopy (XAS), and guided by operando synchrotron x-ray diffraction. During delithiation, Li 2 RuO 3 evolves from a well-defined monoclinic state to a complex trigonal phase via multiple intermediate structures, marked by significant changes in Ru-O bond distances that closely track the transition from a classical cationic redox to an unconventional process centered at oxygen states. Armed with high-quality atomic structural descriptions, computational models of the O K-edge XAS closely reproduce the experimentally observed spectral shifts. Lastly, we relate observations of electrochemical hysteresis with concurrent changes in the pathways of structural and electronic transitions. In conclusion, our results not only clarify the mechanisms underpinning voltage hysteresis in a model for lattice oxygen redox but also underscore the importance of structural fidelity in modeling redox behavior when this type of complex reactivity is present.

Li, Haifeng [Univ. of Illinois, Chicago, IL (Unite↗

The incommensurately modulated structures of low-temperature labradorite feldspars: a single-crystal X-ray and neutron diffraction study

Labradorite feldspars of the plagioclase solid solution series have been known for their complicated subsolidus phase relations and enigmatic incommensurately modulated structures. Characterized by the irrationally indexed e -reflections in the diffraction pattern, e -labradorite shows the largest variation in the incommensurate ordering states among the e -plagioclase structures. The strongly ordered low-temperature e -labradorite is one of the last missing pieces of the e -plagioclase puzzle. Nine plutonic and metamorphic labradorite feldspar samples from Canada, Ukraine, Minnesota (USA), Tanzania and Greenland with compositions ranging from An 52.5 to An 68 were studied with single-crystal X-ray diffraction. Two crystals from Labrador, Canada, and Duluth, MN, USA, with wide enough twin lamellae were analyzed with single-crystal neutron diffraction. The incommensurately modulated structures of e -plagioclase are refined for the first time with neutron diffraction data, which confirmed that the T—O distance modulation in the low-temperature e -plagioclase results from the Al–Si ordering in the framework. Detailed configurations of the M site are also observed in the structures refined from neutron diffraction data, which were not possible to see with X-ray diffraction data. The relation between the q -vectors and the mole% An composition is revealed for the entire compositional range of e -plagioclase, from An 25 to An 75 . The previously proposed two-trend relation depending on the cooling rate and phase transition path is confirmed. A new classification of e -plagioclase ( e α , e β and e γ ) is proposed based on the q -vector of the structure, which makes it an independent character from the presence/absence of density modulation. New parameters are proposed to quantify the ordering states of these complicated aperiodic structures of e -plagioclases, such as the difference between $\langle$T 1 o—O$\rangle$ and $\langle$T 1 m—O$\rangle$ at phase t = 0.2 or the normalized intensity of the (071\bar 1) reflection.

36 MATERIALS SCIENCE↗

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗

The soil pore structure encountered by roots affects plant‐derived carbon inputs and fate

Summary Plant roots are the main supplier of carbon (C) to the soil, the largest terrestrial C reservoir. Soil pore structure drives root growth, yet how it affects belowground C inputs remains a critical knowledge gap. By combining X‐ray computed tomography with 14 C plant labelling, we identified root–soil contact as a previously unrecognised influence on belowground plant C allocations and on the fate of plant‐derived C in the soil. Greater contact with the surrounding soil, when the growing root encounters a pore structure dominated by small (< 40 μm Ø) pores, results in strong rhizodeposition but in areas of high microbial activity. The root system of Rudbeckia hirta revealed high plasticity and thus maintained high root–soil contact. This led to greater C inputs across a wide range of soil pore structures. The root–soil contact Panicum virgatum , a promising bioenergy feedstock crop, was sensitive to the encountered structure. Pore structure built by a polyculture, for example, restored prairie, can be particularly effective in promoting lateral root growth and thus root–soil contact and associated C benefits. The findings suggest that the interaction of pore structure with roots is an important, previously unrecognised, stimulus of soil C gains.

Plant Sciences↗

STRUCTURAL MODELING TO SUPPORT POST-YIELD ACCEPTANCE CRITERIA FOR SPENT NUCLEAR FUEL CLADDING

Spent nuclear fuel (SNF) is evaluated for structural failure during storage and transportation scenarios. The U.S. Department of Energy’s Spent Fuel and Waste Science and Technology (SFWST) program has sponsored significant research in quantifying mechanical loads on SNF during storage and transportation scenarios using experimental and modeling methods. The SFWST program has also performed significant research on measuring the mechanical behavior of irradiated SNF as defueled cladding segments and cladding with fuel pellets to measure composite behavior. This paper considers some of the key material data from the Sibling Pin testing and uses structural modeling and analysis methods that have been informed by testing to consider post-yield acceptance criteria for SNF cladding structural analysis. Test data published by Oak Ridge National Laboratory (ORNL) and Pacific Northwest National Laboratory (PNNL) are the foundation for informing the material behavior of the models developed in this study. In particular, four-point bend (4PB) tests of fueled and defueled cladding segments provide significant information about the bending failure mode of SNF. ORNL’s 4PB test data is on fueled cladding segments, so the composite behavior of SNF is demonstrated. This paper describes PNNL’s coincident beam model that was developed to approximate the composite behavior of SNF. This paper also presents PNNL’s structural dynamic finite element models of a cask tip-over scenario, which is predicted to cause the strongest mechanical loads on SNF of all postulated storage and transportation scenarios. SNF bending loads predicted in the cask tip-over scenario and cladding acceptance criteria beyond yield are considered, with justification based on the Sibling Pin test data. ASME Boiler and Pressure Vessel code stress intensity limits are also considered. The ultimate goal of this work is to aid in the justification of structural acceptance criteria for SNF cladding beyond the cladding’s irradiated yield strength for use in structural analysis of all storage and transportation scenarios.

Klymyshyn, Nicholas A.↗

Fast widefield imaging of neuronal structure and function with optical sectioning in vivo

Optical microscopy, owing to its noninvasiveness and subcellular resolution, enables in vivo visualization of neuronal structure and function in the physiological context. Optical-sectioning structured illumination microscopy (OS-SIM) is a widefield fluorescence imaging technique that uses structured illumination patterns to encode in-focus structures and optically sections 3D samples. However, its application to in vivo imaging has been limited. In this study, we optimized OS-SIM for in vivo neural imaging. We modified OS-SIM reconstruction algorithms to improve signal-to-noise ratio and correct motion-induced artifacts in live samples. Incorporating an adaptive optics (AO) module to OS-SIM, we found that correcting sample-induced optical aberrations was essential for achieving accurate structural and functional characterizations in vivo. With AO OS-SIM, we demonstrated fast, high-resolution in vivo imaging with optical sectioning for structural imaging of mouse cortical neurons and zebrafish larval motor neurons, and functional imaging of quantal synaptic transmission at Drosophila larval neuromuscular junctions.

42 ENGINEERING↗

Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

59 BASIC BIOLOGICAL SCIENCES↗