Structural basis of a distinct α-synuclein strain that promotes tau inclusion in neurons
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Sun, Chuanqi (ORCID:0000000264436407)↗
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Improving the short-wave infrared response of strained GeSn/Ge multiple quantum wells by rapid thermal annealing
In this work, the evolution of structural, optical and optoelectronic properties of coherently strained Ge 0.883 Sn 0.117 /Ge multiple quantum wells (MQWs) grown by molecular beam epitaxy under rapid thermal annealing (RTA) is systematically investigated. The MQW structure remains fully-strained state with RTA at 400 °C or below and disrupts at higher annealing temperatures due to Sn segregation and interdiffusion of Ge and Sn atoms. The GeSn well layers exhibit the strongest absorption in 2.0–2.4 μm after annealing at 400 °C and become transparent above 1.8 μm after RTA at 600 °C or beyond due to serve Sn segregation. Owing to improved crystal quality after RTA at 400 °C, the dark current of the fabricated metal-semiconductor-metal photodetector is effectively lowered by more than two times. Additionally, the responsivities at 1.55 and 2.0 μm are improved by 4.15 and 3.78 folds, respectively, compared to those of the as-grown sample. Here, the results can be an insightful guidance for the development of high-performance short-wave infrared photonic devices based on Sn-containing group-IV low-dimensional structures.
36 MATERIALS SCIENCE↗
Review on the growth, properties and applications of self-assembled oxide–metal vertically aligned nanocomposite thin films—current and future perspectives
Self-assembled oxide–metal nanocomposite thin films have aroused great research interest owing to their wide range of functionalities, including metamaterials with plasmonic and hyperbolic optical properties, and ferromagnetic, ferroelectric and multiferroic behaviors. Oxide–metal nanocomposites typically self-assemble as metal particles in an oxide matrix or as a vertically aligned nanocomposite (VAN) with metal nanopillars embedded in an oxide matrix. Among them, the VAN architecture is particularly interesting due to the vertical strain control and highly anisotropic structure, enabling the epitaxial growth of materials with large lattice mismatch. In this review, the driving forces behind the formation of self-assembled oxide–metal VAN structures are discussed. Specifically, an updated in-plane strain compensation model based on the areal strain compensation concept has been proposed in this review, inspired by the prior linear strain compensation model. It provides a guideline for material selection for designing VAN systems, especially those involving complex orientation matching relationships. Based on the model, several case studies are discussed, comparing the microstructure and morphology of different oxide–metal nanocomposites by varying the oxide phase. Specific examples highlighting the coupling between the electrical, magnetic and optical properties are also discussed in the context of oxide–metal nanocomposites. Finally, future research directions and needs are also discussed.
36 MATERIALS SCIENCE↗
Strain-driven oxygen vacancy ordering in LaNiO 3 thin films revealed by integrated differential phase contrast imaging in scanning transmission electron microscopy
Rare-earth nickelates, such as LaNiO 3 (LNO), exhibit complex electronic properties, with ordered oxygen vacancies (OOV) influencing conductivity and magnetic behavior. We investigate the structural stability of strain-induced OOV phases in LNO thin films grown on SrTiO 3 substrates and the impact of Ruddlesden–Popper (RP) faults. Using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and integrated differential phase contrast (iDPC) STEM imaging, we conducted atomic-scale structural and compositional analyses of OOV. Geometric phase analysis (GPA) was employed to measure the strain in fault-free and RP fault regions, while density functional theory (DFT) calculations explored different OOV arrangements in the LNO phase. Simulated iDPC-STEM imaging of energy-stabilized structures was performed to correlate with experimental results. Here, our findings reveal superstructure modulation in the chemical composition and atomic-scale lattice structure in LNO, primarily due to the formation of the OOV in Ni–O layers of the LaNiO 2.5 phase. The out-of-plane compressive strain of about 2% stabilizes this phase, reducing the strain, diminishing OOV, and transforming them into LNO.
36 MATERIALS SCIENCE↗
Understanding Microstructural Effects on Dynamic Performance Towards the Development of Shock Metamaterials
With the recent advances in additive manufacturing (AM), long-range periodic lattice assemblies are being developed for vibration and shock mitigation components in aerospace and military applications with unique geometric and topological structures. There has been extensive work in understanding the static properties associated with varying topology of these lattice architectures, but there is almost no understanding of microstructural affects in such structures under high-strain rate dynamic loading conditions. Here we report the shock behavior of lattices with varying intrinsic grain structures achieved by post process annealing. High resolution 316L stainless steel lattices were 3D printed by a laser-powder bed fusion machine and characterized by computed tomography. Subsequent annealing resulted in stress-relieved and recrystallized lattices. Overall the lattices had strong cubic texture aligning with the x-, y- and z-directions of the build with a preference outside the build direction (z). The recrystallized sample had more equiaxed polygonal grains and a layer of BCC ferrite at the surface of the structure approximately 1 grain thick. Upon dynamic compression the as-deposited lattice showed steady compaction behavior while the heat-treated lattices exhibit negative velocity behavior indicative of failure. We attribute this to the stiffer BCC ferrite in the annealed lattices becoming damaged and fragmenting during compression.
36 MATERIALS SCIENCE↗
Sparse and Random Sampling Techniques for High-Resolution, Full-Field, BSS-Based Structural Dynamics Identification from Video
Video-based techniques for identification of structural dynamics have the advantage that they are very inexpensive to deploy compared to conventional accelerometer or strain gauge techniques. When structural dynamics from video is accomplished using full-field, high-resolution analysis techniques utilizing algorithms on the pixel time series such as principal components analysis and solutions to blind source separation the added benefit of high-resolution, full-field modal identification is achieved. An important property of video of vibrating structures is that it is particularly sparse. Typically video of vibrating structures has a dimensionality consisting of many thousands or even millions of pixels and hundreds to thousands of frames. However the motion of the vibrating structure can be described using only a few mode shapes and their associated time series. As a result, emerging techniques for sparse and random sampling such as compressive sensing should be applicable to performing modal identification on video. This work presents how full-field, high-resolution, structural dynamics identification frameworks can be coupled with compressive sampling. The techniques described in this work are demonstrated to be able to recover mode shapes from experimental video of vibrating structures when 70% to 90% of the frames from a video captured in the conventional manner are removed.
47 OTHER INSTRUMENTATION↗
Visualization of the strain-induced topological phase transition in a quasi-one-dimensional superconductor TaSe 3
Control of the phase transition from topological to normal insulators can allow for an on/off switching of spin current. While topological phase transitions have been realized by elemental substitution in semiconducting alloys, such an approach requires preparation of materials with various compositions. Thus it is quite far from a feasible device application, which demands a reversible operation. In this work, we use angle-resolved photoemission spectroscopy and spin- and angle-resolved photoemission spectroscopy to visualize the strain-driven band-structure evolution of the quasi-one-dimensional superconductor TaSe 3 . We demonstrate that it undergoes reversible strain-induced topological phase transitions from a strong topological insulator phase with spin-polarized, quasi-one-dimensional topological surface states, to topologically trivial semimetal and band insulating phases. The quasi-one-dimensional superconductor TaSe 3 provides a suitable platform for engineering the topological spintronics, for example as an on/off switch for a spin current that is robust against impurity scattering.
36 MATERIALS SCIENCE↗
Quasi-Extended Range Optical Frequency Domain Reflectometry for Product Pipelines
Throughout the United States, large natural gas and product transmission pipelines exist. These pipelines are susceptible to failure through corrosion and cracking due to internal and external factors. As these transmission pipeline age, the likelihood of a catastrophic failure increases. The ability to the monitor corrosion and wall thickness of these pipelines is paramount to reduce risk of disastrous failure and increase reliability as well as safety. Optical frequency domain reflectometry can monitor distributed temperature and strain measurements along the natural gas and product pipelines. This measurement technique can provide valuable information of pipe structural health through hoop strain changes due to pipe wall thinning, temperature changes due to gas leaks based on Joule-Thomson effect. Since these pipelines are typically buried, the depth of the pipeline results in a potential loss in the sensing range where the fiber is not physically monitoring the hoop strain of the pipeline. A different configuration of the interferometer will allow for the distributed fiber measurement to start atop the pipeline itself. This configuration results in no loss of sensing range and maintains the sensing resolution of a typically interferometer for an optical frequency domain reflectometry measurement. The quasi-extended range distributed hoop strain measurements were demonstrated on an active transmission pipeline.
Brister, Matthew↗
Crystal structure of a putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 Å resolution
Syntrophus aciditrophicus strain SB is a model syntroph that degrades benzoate and alicyclic acids. Here, the structure of a putative 3-hydroxypimelyl-CoA dehydrogenase from S. aciditrophicus strain SB (SaHcd1) was resolved at 1.78 Å resolution. SaHcd1 contains sequence motifs and structural features that belong to the short-chain dehydrogenase/reductase (SDR) family of NADPH-dependent oxidoreductases. SaHcd1 is proposed to concomitantly reduce NAD + or NADP + to NADH or NADPH, respectively, while converting 3-hydroxypimelyl-CoA to 3-oxopimeyl-CoA. Further enzymatic studies are needed to confirm the function of SaHcd1.
59 BASIC BIOLOGICAL SCIENCES↗
MODELING A SPENT NUCLEAR FUEL CASK SEISMIC TEST
The US Department of Energy Spent Fuel and Waste Science and Technology (SFWST) program is planning to conduct a series of full-scale shake table tests to simulate hypothetical earthquake conditions and record the response of surrogate spent nuclear fuel (SNF) assemblies in a canister dry storage system mockup. The shake table motions will represent a range of hypothetical earthquake conditions at hypothetical locations in the continental US to generally define the range of mechanical loads that SNF can be expected to experience during extended dry storage periods. The earthquake conditions will represent seismic hazards in the 2,000-to-20,000-year return period range. The test will use instrumented pressurized water reactor fuel assemblies with surrogate mass inside the fuel rods instead of radioactive fuel pellets. Dummy assemblies with similar mass and dimensions to actual fuel assemblies will occupy the rest of the fuel assembly locations in a SNF canister that holds 32 fuel assemblies. The canister will be located inside a mockup vertical concrete cask. Instrumentation will record the motion of the major components of the complex dynamic system, and strain gauges will be used to record the cladding strain at select locations. Preparations for the test require modeling predictions to identify the range of response of the system and to help select specific earthquake cases to be simulated on the shake table from a large set of potential cases. This paper describes the pretest nonlinear finite element modeling efforts that have been completed to date, including cask system level modeling and fuel assembly modeling in LS-DYNA. The cask system level models are critical for anticipating sliding or tipping of an unanchored cask during the test. The fuel assembly model is needed to estimate the range of cladding strain response and fuel assembly structural response to be expected during the test and cladding strain measurements will be key metrics for model validation and the development of modeling best practices after the test is concluded.
Klymyshyn, Nicholas A.↗
Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2
Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X -Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.
59 BASIC BIOLOGICAL SCIENCES↗
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1
The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold ; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.
Bragagnolo, Nicholas↗
Quantum Photon Sources in WSe 2 Monolayers Induced by Weakly Localized Strain Fields
Quantum emitters in semiconductor transition metal dichalcogenide (TMD) monolayers hold great promise for many quantum optics applications due to the intriguing properties afforded by the host materials. The creation of localized excitonic states in two-dimensional semiconductors is also fundamentally interesting. Local strain engineering of TMD monolayers has been attested to be a viable approach for creating quantum emitters. However, despite the ubiquitous existence of local topography variations in the structures used to create strain gradients in the TMD monolayers, an understanding of their influence on the strain fields and exciton trapping is notably lacking, especially on the nanoscale. In this study, we investigate WSe 2 monolayers deposited on the edges of asfabricated trenches, which are deemed to induce 1D delocalized strain profiles in the monolayers, and observe optical signatures of weakly confined excitonic states supporting biexciton emission. Here, our numerical simulations of the strain distributions suggest that the quantum emitters originate from quasi-1D like localized strain profiles induced by local topography variations at the trench edges. These findings have strong implications toward the controlled creation of quantum emitters in TMD monolayers and their efficient coupling to photonic structures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhanced optoelectronic and elastic responses in fluorinated penta-BCN
We report surface passivation in two-dimensional (2D) materials is one of the best approaches to modulate the structural, dynamical, and mechanical stabilities thereby enhancing chemical and physical properties for optoelectronic applications. Here, we report an ab-initio investigation on structurally, thermally, dynamically, and mechanically stable, and experimentally feasible fluorinated penta-BCN (F-BCN) monolayer. The structural reconstruction after fluorination, increases bond lengths and thickness to reduce the average stiffness and elasticity attaining the mechanical isotropy. Nevertheless, the value of 2D Young’s modulus of F-BCN is comparable to the pristine structure at 6% of compression without mechanical instability. A significant bandgap tailoring is achieved, similar to that of mechanical sensitivity, due to applied strain. Remarkably, following the fluorine passivation, the monolayer’s induced wide direct bandgap semiconducting behavior improves optical absorbance and reflectivity, decreases energy loss, changes optical anisotropy, and makes it a promising candidate material for optoelectronic and nanomechanical applications.
36 MATERIALS SCIENCE↗
Towards computational polar-topotronics: Multiscale neural-network quantum molecular dynamics simulations of polar vortex states in SrTiO3/PbTiO3 nanowires
Recent discoveries of polar topological structures ( e.g ., skyrmions and merons) in ferroelectric/paraelectric heterostructures have opened a new field of polar topotronics. However, how complex interplay of photoexcitation, electric field and mechanical strain controls these topological structures remains elusive. To address this challenge, we have developed a computational approach at the nexus of machine learning and first-principles simulations. Our multiscale neural-network quantum molecular dynamics molecular mechanics approach achieves orders-of-magnitude faster computation, while maintaining quantum-mechanical accuracy for atoms within the region of interest. This approach has enabled us to investigate the dynamics of vortex states formed in PbTiO 3 nanowires embedded in SrTiO 3 . We find topological switching of these vortex states to topologically trivial, uniformly polarized states using electric field and trivial domain-wall states using shear strain. These results, along with our earlier results on optical control of polar topology, suggest an exciting new avenue toward opto-electro-mechanical control of ultrafast, ultralow-power polar topotronic devices.
Linker, Thomas↗
Localized Flexoelectric Effect Around Ba(CuNb) Nano‐Clusters in Epitaxial BiFeO 3 Films for Enhancement of Electric and Multiferroic Properties
Abstract Room‐temperature (RT) multiferroic materials have received significant research attention for various potential applications; however, their properties are not suitable for real‐world implementation. In this study, a nano‐scale localized flexoelectric effect is introduced to enhance the RT multiferroic performance of epitaxial bismuth iron oxide (BiFeO 3 ; BFO) thin films by embedding 10 mol% Ba(Cu 1/3 Nb 2/3 )O 3 (BCN) nano‐clusters into the host BFO film, which originally has a rhombohedral crystal structure. By utilizing nano‐clustering, a large out‐of‐plane coherent strain is localized around the nano‐clusters, resulting in a highly strained tetragonality of the BFO structure; subsequently, the films exhibit peculiar types of domains and domain walls, such as nano‐scale rotational vortices and antiparallel dipole configurations. These peculiar domain structures, which originate from the localized flexoelectric effect at the nano‐scale, enable excellent ferroelectric, ferromagnetic, and RT multiferroic magnetoelectric coupling. This study reveals that the local variation in the localized flexoelectric field around nano‐clusters considerably impacts the formation of unusual domain‐wall structures. This suggests that the controlled introduction of nano‐clusters with different crystal structures is promising for achieving the desired multiferroic properties.
Song, Hyunseok↗
High-pressure characterization of Ag 3 AuTe 2 : Implications for strain-induced band tuning
Recent band structure calculations have suggested the potential for band tuning in the chiral semiconductor Ag 3 AuTe 2 to zero upon application of negative strain. In this study, we report on the synthesis of polycrystalline Ag 3 AuTe 2 and investigate its transport and optical properties and mechanical compressibility. Transport measurements reveal the semiconducting behavior of Ag 3 AuTe 2 with high resistivity and an activation energy E a of 0.2 eV. The optical bandgap determined by diffuse reflectance measurements is about three times wider than the experimental E a . Despite the difference, both experimental gaps fall within the range of predicted bandgaps by our first-principles density functional theory (DFT) calculations employing the Perdew–Burke–Ernzerhof and modified Becke–Johnson methods. Furthermore, our DFT simulations predict a progressive narrowing of the bandgap under compressive strain, with a full closure expected at a strain of –4% relative to the lattice parameter. To evaluate the feasibility of gap tunability at such substantial strain, the high-pressure behavior of Ag 3 AuTe 2 was investigated by in situ high-pressure x-ray diffraction up to 47 GPa. Mechanical compression beyond 4% resulted in a pressure-induced structural transformation, indicating the possibility of substantial gap modulation under extreme compression conditions.
36 MATERIALS SCIENCE↗
Host Onboarding Tool (HObT) v1.0.0
The Host OnBoarding Tool (Hobt) is a publicly accessible, web-based software designed to organize and share information about microbial hosts under development at the Agile BioFoundry (ABF). It streamlines the assessment, tracking, and sharing of information related to microbial host development and provides a centralized platform where users can rapidly evaluate hosts' readiness for various bio processes. HObT leverages the Tier System, a standardized host development framework that organizes and assesses microbial hosts based on their readiness for biomanufacturing. Each tier outlines key targets—including genetic tools, growth conditions, omics data, and predictive models—needed to transform new or emerging microbes into established production platforms. By applying clear criteria for advancement, the Tier System helps users quickly evaluate each organism's current development status, identify gaps in available knowledge or tools, and prioritize future strain improvement efforts. Through its user-friendly interface, HObT encourages contributions of new data and insights from researchers, fostering collaboration and accelerating host development. By providing structured guidance for microbial strain advancement, HObT and the Tier System support more systematic, rapid, and cost-effective development of non-traditional microbial hosts, ultimately enhancing the efficiency and impact of biomanufacturing research and applications.
Plahar, Hector [Lawrence Berkeley National Laborat↗