Blind, simultaneous identification of full-field vibration modes and large rigid-body motion of output-only structures from digital video measurements
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Yang, Yongchao (ORCID:0000000317763306)↗
SEARCH · Engineering Papers
Results for “structural modes”
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Absence of magnetoelastic deformation in the spin-chain compound CuBr 2
Here, we investigate a spin-$\frac{1}{2}$ antiferromagnet, CuBr 2 , which has quasi-one-dimensional structural motifs. The system has previously been observed to exhibit unusual Raman modes possibly due to a locally deformed crystal structure driven by the low-dimensional magnetism. Using hard x-ray scattering and neutron total scattering, here we aim to verify a specific form of tetramerizing deformation proposed in the previous study. Apart from diffuse scattering signals, which we can reproduce by performing a thorough modeling of the lattice's thermal vibrations, we do not observe evidence for a tetramerized lattice structure within our detection sensitivity. Consequently, we consider it unlikely that the unusual Raman modes in CuBr 2 arise from quantum spin-singlet-driven lattice deformations.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain
Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
59 BASIC BIOLOGICAL SCIENCES↗
A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'- O methylation of its first nucleotide
The SARS-CoV-2 nsp16/nsp10 enzyme complex modifies the 2'-OH of the first transcribed nucleotide of the viral mRNA by covalently attaching a methyl group to it. The 2'-O methylation of the first nucleotide converts the status of mRNA cap from Cap-0 to Cap-1, and thus, helps the virus evade immune surveillance in host cells. Here, we report two structures of nsp16/nsp10 representing pre- and post-release states of the RNA product (Cap-1). We observe overall widening of the enzyme upon product formation, and an inward twisting motion in the substrate binding region upon product release. These conformational changes reset the enzyme for the next round of catalysis. The structures also identify a unique binding mode and the importance of a divalent metal ion for 2'-O methylation. We also describe underlying structural basis for the perturbed enzymatic activity of a clinical variant of SARS-CoV-2, and a previous SARS-CoV outbreak strain.
60 APPLIED LIFE SCIENCES↗
A direct numerical simulation of Jet A flame kernel quenching
The safe operation of aeronautical engines requires an understanding of flame ignition, propagation and extinction. In this study, direct numerical simulations are performed using a 29 species reduced chemical mechanism for jet fuel surrogate Jet A to understand the flame quenching process. Here, initially laminar spherical flames of varying sizes and equivalence ratios are subject to an identical periodic domain of decaying and isotropic high intensity turbulence with a turbulent Reynolds number of 2400. All cases become quenched, except for the larger kernel with lower Karlovitz number. An analysis of the flame structure shows broadened preheat zone, flame shortening on the product side, differential species diffusion and partial fuel pyrolysis in the fresh mixture. Two extinction mechanisms are identified arising from flame shortening and high flame stretch. Flame shortening occurs due to turbulence-chemistry interactions that resemble the flame–flame interaction in a laminar counterflow reactant-to-reactant configuration, which contorts and breaks up the ignition kernel. Flame stretch is a local effect that attenuates the heat release rate and causes the flame to retreat towards the product mixtures, similar to what has been observed for reactant-to-product laminar counterflow flames. Chemical explosive mode analysis was also performed to quantify the flame structure and local combustion mode. The diffusion–reaction balance in pinched-off flame islands favors extinction of these smaller structures, while auto-ignition modes are observed within the flame kernel after fresh mixture is engulfed and preheated in the product kernel. Statistics of the density-weighted displacement speed conditional on local combustion mode indicates strong correlation between the local extinction mode and negative displacement speed. The local balance between diffusion and reaction ultimately determines the propensity for local extinction in both laminar and turbulent flames, the extent of which has an impact on global flame propagation.
42 ENGINEERING↗
Low-threshold, single-transverse-mode, 940-nm vertical-cavity surface-emitting laser with a mode filter and half-wavelength cavity
We demonstrate a structure for a vertical-cavity surface-emitting laser (VCSEL) with a mode filter and half-wavelength (λ/2) cavity. The effects of λ/2- and λ-cavities on the threshold current are studied. The thickness and etched diameter of the mode filter are optimised to achieve single-transverse-mode output. The results show that when changing from λ-cavity to λ/2-cavity, the threshold current of the VCSEL decreases by 30.7% (from 0.85 mA to 0.65 mA). In addition, for the mode-filter thickness of 80 nm, and the etched diameter of 2.5 μm, the side mode suppression ratio reaches 90 dB, which meets the requirement of single-transverse-mode output. The VCSELs with the optimised design can overcome many difficulties and have great potential in 3D face recognition. (paper)
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding
Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Further, characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.
60 APPLIED LIFE SCIENCES↗
The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants
Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Monitoring of corrosion effects in pipes with multi-mode acoustic signals
Current commercial long-range guided wave inspection and monitoring technologies for pipes usually require establishment of certain specific acoustic modes for wave propagation and use a large number of sensors in a certain geometric arrangement (for example, uniformly-spaced arrays of sensors on a collar, placed around a pipe). This paper, in contrast, presents a long-range corrosion detection method in pipes based on multi-mode guided acoustic waves, generated and received using simple, single-element sensors. In this technique, available guided wave modes in any interrogated zone of the structure are automatically down-selected by the medium, and changes in energy distribution over the selected modes are analyzed through signal processing to monitor material loss or addition. Here, to investigate the feasibility of the proposed method, we have performed both experimental and numerical simulation studies on 50.8-mm (2-in)-diameter schedule-40 carbon steel pipes. In these studies, a linear chirp signal is injected in compression mode, perpendicular to the surface of the pipe, generating multi-mode, multi-directional guided waves that travel within the pipe wall. Corrosion effects in the pipes are simulated numerically and experimentally. To reduce errors in the measurement technique due to changes in the local or global temperature of the measured media, a universal temperature compensation algorithm is introduced. The experimental results show good agreement with simulation results, indicating that the proposed multi-mode wave generation and detection in a pipe could be used for long-range detection and monitoring of corrosion effects, such as pipe wall losses or solid material deposits.
36 MATERIALS SCIENCE↗
Analysis of First-Order Gratings in Silicon Photonic Waveguides
A simple thin film effective index analysis for first order gratings in Si photonic waveguides is shown to provide highly accurate results for reflected and transmitted power spectrums as long as the waveguide remains single mode and non-radiating. A cover layer can be added to the grating region of a Si photonic waveguide to increase the strength of the grating, modify transition losses from the input waveguide to the grating waveguide region, and/or modify the width of the reflectivity spectrum. For a given grating period, the peak reflection and spectral width of the reflectivity decrease as the duty cycle is decreased or increased from ~50%. For both radiating and multimode structures, the coupling between all modes, power radiated towards the superstrate (upwards), power radiated downwards (substrate) and transmitted power analyzed by Floquet-Bloch, Eigenmode Expansion and Finite Difference Time Domain methods show excellent agreement. Coupling coefficients calculated using analytic formulas are shown to be accurate only for shallow grating depths.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Increased localization of Majorana modes in antiferromagnetic chains on superconductors
Magnet-superconductor hybrid (MSH) systems are a key platform for custom-designed topological superconductors. Ideally, the ends of a one-dimensional MSH structure will host Majorana zero-modes (MZMs), the fundamental unit of topological quantum computing. However, some experiments with ferromagnetic (FM) chains show a more complicated picture. Due to tiny gap sizes and hence long coherence lengths, MZMs might hybridize and lose their topological protection. Recent experiments on a niobium surface have shown that both FM and antiferromagnetic (AFM) chains may be engineered, with the magnetic order depending on the crystallographic direction of the chain. While FM chains are well understood, AFM chains are less so. Here, we study two models inspired by the niobium surface: A minimal model to elucidate the general topological properties of AFM chains and an extended model to more closely simulate a real system by mimicking the proximity effect. Here, we find that, in general, for AFM chains, the topological gap is larger than for FM ones, and thus, coherence lengths are shorter for AFM chains, yielding more pronounced localization of MZMs in these chains. While for some parameters AFM chains may be topologically trivial, we find in these cases that adding an adjacent chain can result in a nontrivial system, with a single MZM at each chain end.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Large Area Detection of Microstructural Defects with Multi-Mode Ultrasonic Signals
Cyclic loading or other stresses can lead to development of cracks and crack growth in mechanical structures, leading to eventual failure. While ultrasound imaging can be used for non-destructive testing of such structures, conventional ultrasound techniques are often limited by crack size, density, and areal coverage. An effective characterization of real-world, large-area structures is required at an early damage stage to prevent catastrophic failure and predict remaining life. In this study, a new nonlinear ultrasonic testing (NUT) method is proposed for large-area monitoring of practical structures with arbitrary complexity by using multiple-mode guided-wave ultrasonic signals. The proposed guided-wave NUT technique requires single-element transducers, simple electronics, and a mixed time-frequency domain signal processing. As a proof-of-concept demonstration, numerical simulations and experiments are performed on an A36 carbon steel beam assembly with previously formed microstructural defects that cause nonlinearities in ultrasonic response. The quadratic dependence of the nonlinear wave excitation on the input ultrasonic signal amplitude is shown by numerical simulations, and such a nonlinear ultrasonic response is experimentally observed in the zone with a high density of microstructural defects.
36 MATERIALS SCIENCE↗
Variational study of the Kitaev-Heisenberg-Gamma model
Here we compute the low-energy excitation spectrum and the dynamical spin structure factor of the Kitaev-Heisenberg-Gamma model through a variational approach based on the exact fractionalized excitations of the pure Kitaev honeycomb model. This novel approach reveals the physical reason for the asymmetric stability of the Kitaev spin liquid phases around the ferromagnetic and antiferromagnetic Kitaev limits. Moreover, we demonstrate that the fractionalized excitations form bound states in specific regions of each Kitaev spin liquid phase and that certain phase transitions induced by Heisenberg and Gamma interactions are driven by the condensation of such a bound state. Remarkably, this bound state appears as a sharp mode in the dynamical spin structure factor, while its condensation patterns at the appropriate phase transitions provide a simple explanation for the magnetically ordered phases surrounding each Kitaev spin liquid phase.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers
ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
Biochemistry & Molecular Biology↗
Cosolvent-tuned interactions in ionic liquids: A vibrational and quantum-chemical study of ethylene glycol ratio effects
Ionic liquids (ILs) are attractive media for CO 2 capture but remain limited by viscosity and cost. Blending ILs with ethylene glycol (EG) is a practical route to mitigate these constraints, yet the molecular origins of cosolvent effects and their dependence on composition are not well resolved. We combine Fourier-transform infrared (FT-IR) spectroscopy with quantum-chemical (DFT) analysis to elucidate how the IL:EG molar ratio modulates intermolecular interactions and electronic structure. Computed vibrational frequencies enable mode assignment and deconvolution of overlapping bands, revealing systematic, ratio-dependent shifts and broadenings in (i) EG O–H stretching, (ii) cation and EG C–H stretchings (imidazolium C2–H, C4–H, C5–H, methyl and ethyl groups, -CH2 of EG), (iii) anion signature modes (e.g., CN motifs), and (iv) EG C–O and C–C stretchings, consistent with the redistribution of hydrogen-bonding networks. Molecular electrostatic potential (MESP) maps quantify attenuation of extreme potential regions with increasing EG, indicating progressive screening of cation–anion electrostatic interactions. Quantum Theory of Atoms in Molecules (QTAIM) identifies emergent bond critical points between EG and the IL ions, while Reduced Density Gradient–Noncovalent Interaction (RDG–NCI) analysis differentiates strong directional hydrogen bonds from dispersive contacts across compositions. Together, these results show that EG fraction controls a switch from predominantly ion–ion to mixed ion–EG coordination, altering local polarity and polarizability that underlie the observed FT-IR trends. The framework provides composition–structure–spectrum relationships that can guide rational selection of IL:EG ratios to balance favorable molecular interactions with practical performance targets in scalable CO 2 capture systems.
DAC↗
Texture Analysis of Inconel 718 with Different Modes During Single-Track Laser Surface Re-Melting
An in-depth understanding of the texture formation in melt pools allows for the modification of the surface layer microstructure and corresponding material properties, providing an opportunity to integrate laser surface re-melting into metal additive manufacturing. This study investigates crystallographic texture formation at different cooling rates in single melting tracks on the Inconel 718 (IN718) plate produced by laser surface re-melting. The cooling rate varies from 2.31 × 10 5 °C/s to 9.56 × 10 5 °C/s with the increase in scanning rates from 400 mm/s to 1200 mm/s, measured by recently developed real-time temperature monitoring of melt pools. Columnar grains are dominant, with distinct crystallographic textures forming in the melt pools. At a slower scanning speed, the keyhole mode shows three different textures forming at different depths (crystallographically layered structure), while, at a faster scanning speed, the conduction mode shows only random grain orientation. There are no pores/voids detected, and the columnar grain morphology and columnar grain width (8.6 μm to 12.4 μm) follow the analysis framework in terms of thermal gradient and solidification rate analysis. This implies that laser surface re-melting provides the potential to modify the surface structure from a random grain orientation to a crystallographically layered structure.
36 MATERIALS SCIENCE↗
First principles modeling of polymer encapsulant degradation in Si photovoltaic modules
An outstanding issue in the longevity of photovoltaic (PV) modules is the accelerated degradation caused by the presence of moisture. Moisture leads to interfacial instability, de-adhesion, encapsulant decomposition, and contact corrosion. However, experimental characterization of moisture in PV modules is not trivial and its impacts can take years or decades to establish in the field, presenting a major obstacle to designing high-reliability modules. First principles calculations provide an alternative way to study the ingress of water and its detrimental effect on the structure and decomposition of the polymer encapsulant and interfaces between the encapsulant and the semiconductor, the metal contacts, or the dielectric layer. Here, we use density functional theory (DFT) computations to model single chain, crystalline and cross-linked structures, infrared (IR) signatures, and degradation mechanisms of ethylene vinyl acetate (EVA), the most common polymer encapsulant used in Si PV modules. IR-active modes computed for low energy EVA structures and possible decomposition products match well with reported experiments. The EVA decomposition energy barriers computed using the Nudged Elastic Band (NEB) method show a preference for acetic acid formation as compared to acetaldehyde, are lowered in the presence of a water solvent or hydroxyl ion catalyst, and match well with reported experimental activation energies. This systematic study leads to a clear picture of the hydrolysis-driven decomposition of EVA in terms of energetically favorable mechanisms, possible intermediate structures, and IR signatures of reactants and products.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure-based optimization of hydroxylactam as potent, cell-active inhibitors of lactate dehydrogenase
Structure-based design was utilized to optimize 6,6-diaryl substituted dihydropyrone and hydroxylactam to obtain inhibitors of lactate dehydrogenase (LDH) with low nanomolar biochemical and single-digit micromolar cellular potencies. Surprisingly the replacement of a phenyl with a pyridyl moiety in the chemical structure revealed a new binding mode for the inhibitors with subtle conformational change of the LDHA active site. Finally, this led to the identification of a potent, cell-active hydroxylactam inhibitor exhibiting an in vivo pharmacokinetic profile suitable for mouse tumor xenograft study.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗