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At least 325 records · Page 18

Combining geometric-optical and spectral invariants theories for modeling canopy fluorescence anisotropy

The spectral invariants theory ( p -theory) has received much attention in the field of quantitative remote sensing over the past few decades and has been adopted for modeling of canopy solar-induced chlorophyll fluorescence (SIF). However, the spectral invariant properties (SIP) in simple analytical formulae have not been applied for modeling canopy fluorescence anisotropy primarily because they are parameterized in terms of leaf total scattering, which precludes the differentiation between forward and backward leaf SIF emissions. In this study, we have developed the canopy-SIP SIF model by combining geometric-optical (GO) theory to account for asymmetric leaf SIF forward and backward emissions at the first-order scattering and by modeling multiple scattering based on the p-theory, thus avoiding the dependence on radiative transfer models. The applicability of the model simulations especially over 3D heterogeneous canopies was improved by incorporating canopy structure through multi-angular clumping index, and by modeling single scattering from the four components of the scene in view according to the GO approach. The results show good consistency with both the state-of-the-art SIF models and multi-angular field SIF observations over grass and chickpea canopies. Further, the coefficient of determination (R²) between the simulated SIF and field measurements was 0.75 (red) and 0.74 (far-red) for chickpea, and 0.65 (both red and far-red) for grass. The average relative error was approximately 3% for 1D homogeneous scenes when comparing the canopy-SIP SIF model simulations to the SCOPE model simulations, and around 4% for the 3D heterogeneous scene when comparing to the LESS model simulations. The results indicate that the proposed approach for separating asymmetric leaf SIF emissions is a robust way to keep a balance between satisfactory simulation accuracy and efficiency. Model simulations suggest that neglecting the leaf SIF asymmetry can lead to an underestimation of canopy red SIF by 6.3% to 42.6% for various leaf biochemical and canopy structural parameters. This study presents a simple but efficient analytical approach for canopy fluorescence modeling, with potential for large-scale canopy fluorescence simulations.

3D heterogeneous structure↗

Durability of plasma sprayed Thermal Barrier Coatings with controlled properties part Ⅱ: Effects of geometrical curvature

The present investigation elucidates the effects of substrate curvature on the durability of Air Plasma Sprayed (APS) Thermal Barrier Coatings (TBCs). Traditionally, planar disk specimens are utilized in Furnace Cycle Testing (FCT). In most cases, delamination is initiated at the disk's free edge and then propagates along the TBC-bond coat interface. However, in turbine components (e.g., blades/vanes), they lack significant free edges and the coatings are deposited on non-flat surfaces of varying radii of curvature. These geometrical discrepancies imply significant differences in the stress states as compared to planar disk specimens. Therefore, the part geometry inevitably affects the TBC failure mechanisms in the turbine system, and consequently influences TBC durability. Nevertheless, these effects have not been fully explored in the past, despite the anecdotal knowledge which suggests the leading edge of turbine blades to be one of the most common failure/spallation locations. Here in this study, representative TBC systems were deposited onto superalloy disks with flat substrate and rods with curved substrate. The experimental results from FCT suggest TBC durability on rods is significantly lower than when sprayed on disks. Furthermore, the durability of TBCs on rods appears to increase with higher porosity, which is contradictory to reported trends for TBCs on disks. In addition, the effects of various bond coats are not consistent with those observed in disks. To clarify the underlying effects of curved geometries, detailed stress analyses were performed. They revealed a state of thermal stresses which is unique to curved geometries. It was found that TBC on rods experience tensile radial stresses as well as tensile hoop stresses during the cooling. These stresses result in a complex interplay in failure processes in rods, which explains the different observed trends in the durability from those obtained with disks.

36 MATERIALS SCIENCE↗

Geometric control of emergent antiferromagnetic order in coupled artificial spin ices

Artificial spin ices (ASIs) composed of coupled nanomagnets offer the possibility to create designer geometrical frustration and manipulate inter-nanomagnet interactions. In particular, by using a dimer motif consisting of two strongly coupled single-domain nano magnets as a building block, we can control and realize intriguing antiferromagnetic physical states in which the magnetic charge is not conserved. Here we create a dimer kagome ASI system within which the antiferromagnetic order is controlled by tuning lattice geometry. Different disordered antiferromagnetic phases and the inter-nanomagnet interactions are visualized directly in demagnetized lattices with different lattice parameters. Monte Carlo simulations establish that the collective ground state consists of disordered antiferromagnetic dimers across the lattice when the intra-dimer interaction is dominant. However, for lattices governed by intra-triad-unit interactions, the ground state exhibits a longrange spin-ordered state in which the vertex magnetic charge is uniform across all triads.

36 MATERIALS SCIENCE↗

Characterization and interaction of geometric and contact/impact nonlinearities in dynamical systems

Here, we study how a contact/impact nonlinearity interacts with a geometric cubic nonlinearity in an oscillator system. Specific focus is shown to the effects on bifurcation behavior and secondary resonances (i.e., super- and sub-harmonic resonances). The effects of the individual nonlinearities are first explored for comparison, and then the influences of the combined nonlinearities, varying one parameter at a time, are analyzed and discussed. Nonlinear characterization is then performed on an arbitrary system configuration to study super- and sub-harmonic resonances and grazing contacts or bifurcations. Both the cubic and contact nonlinearities cause a drop in amplitude and shift up in frequency for the primary resonance, and they activate high-amplitude subharmonic resonance regions. The nonlinearities seem to never destructively interfere. The contact nonlinearity generally affects the system’s superharmonic resonance behavior more, particularly with regard to the occurrence of grazing contacts and the activation of many bifurcations in the system’s response. The subharmonic resonance behavior is more strongly affected by the cubic nonlinearity and is prone to multistable behavior. Perturbation theory proved useful for determining when the cubic nonlinearity would be dominant compared to the contact nonlinearity. The limiting behaviors of the contact stiffness and freeplay gap size indicate the cubic nonlinearity is dominant overall. It is demonstrated that the presence of contact may result in the activation of several bifurcations. In addition, it is proved that the system’s subharmonic resonance region is prone to multistable dynamical responses having distinct magnitudes.

42 ENGINEERING↗

Geometrical optics without singularities: using the ray time as the coordinate space

Geometrical optics (GO) is widely used for reduced modelling of waves in plasmas, but it fails near reflection points, where it predicts a spurious singularity of the wave amplitude. We show how to avoid this singularity by adopting a different representation of the wave equation. Instead of the physical coordinate 𝑥 and the wavevector 𝑘, we use the ray time 𝜏 as the new canonical coordinate and the ray energy ℎ as the associated canonical momentum. To derive the envelope equation in the 𝜏-representation, we construct the Weyl symbol calculus on the (𝜏,ℎ) space and show that the corresponding Weyl symbols are related to their (𝑥,𝑘) counterparts by the Airy transform. This allows us to express the coefficients in the envelope equation through the known properties of the original dispersion operator. When necessary, solutions of this equation can be mapped to the 𝑥-space using a generalised metaplectic transform. However, the field per se might not even be needed in practice. Instead, knowing the corresponding Wigner function usually suffices for linear and quasilinear calculations. As a Weyl symbol itself, the Wigner function can be mapped analytically, using the aforementioned Airy transform. We show that the standard Airy patterns that form in regions where conventional GO fails are successfully reproduced within metaplectic GO (MGO) simply by remapping the field from the 𝜏-space to the 𝑥-space. An extension to mode-converting waves is also presented. This formulation, which we call generalised MGO, can be particularly useful, for example, for reduced modelling of the O–X conversion in inhomogeneous plasma near the critical density, an effect that is important for fusion applications and also occurs in the ionosphere. Overall, MGO can replace GO for any practical purposes, because it better handles cutoffs and is similar otherwise.

plasma waves↗

Interpretation of high-harmonic fast-wave propagation in the scrape-off layer of NSTX-U as a geometrically bounded-waveguide mode

This paper revisits the onset of high-harmonic fast-wave (HHFW) propagation in the scrape-off layer (SOL) plasma of the NSTX/NSTX-U spherical tokamak, motivated by past HHFW heating and current drive experiments and modelling. Previously, the fast-wave propagation in the SOL was correlated with the opening (suppression) of the fast-wave right-hand cutoff layer in front of the antenna. In this work, the SOL propagation is interpreted as a geometric waveguide mode guided by the SOL geometry, whose radial width can be comparable to the wave’s perpendicular wavelength in the HHFW regime. A two-dimensional circular model is first employed using full-wave solvers to characterise the poloidal eigenmode structures and to clarify their relationship to annulus resonance. By progressively adding a tokamak-like magnetic-field configuration, starting from a uniform axial field, the effects of magnetic-field gradients and pitch on the SOL waveguide mode are characterised. The poloidal mode numbers supported by the SOL plasma agree well with analytic estimates, indicating that an anisotropic plasma in a bounded geometry selectively supports and amplifies the resonant poloidal mode number. Additionally, two-dimensional axisymmetric NSTX-U simulations demonstrate that the SOL eigenmode features identified in the circular model persist in the experimentally relevant configurations. A control approach based on lengthening the wave perpendicular wavelength relative to the SOL width, including a higher magnetic (B)-field operation, is discussed. The analysis here shows the key role of a bounded geometry in interpreting HHFW eigenmode coupling and propagation in the NSTX-U SOL plasma.

plasma heating↗

Relating Geometric Nanoconfinement and Local Molecular Environment to Diffusion in Ionic Polymer Membranes

Understanding structure-diffusion relationships in ionic polymer membranes not only illuminates fundamental mechanisms for membrane transport, but also informs further membrane development. In this study, we employ NMR diffusometry and molecular dynamics (MD) simulations to investigate diffusion coefficients and activation energies of diffusion (Ea) for both a lithium-form perfluorosulfonic acid membrane and aqueous solutions of lithium triflate. NMR shows that, at high water/ion molar ratio (?), Ea for water diffusion is slightly lower in the membrane than in solution. Conversely, membrane transport exhibits much higher Ea at low hydration as compared to solutions. MD simulations of a model system consisting of carbon nanotubes with varying diameter reveal that Ea of diffusion clearly relates to both the geometric nanoconfinement of the hydrophilic pathways in the membrane as well as the local molecular environment. These results demonstrate that Ea of diffusion can serve as a revelatory tool for the study of molecular transport processes and the coupling of morphology with transport at the nanoscale. This study thus provides new insights and new experimental and computational models for understanding transport in a wide range of polymer membranes, such as those used in molecular separations applications.

Zhang, Rui↗

Geometric transformation and three-dimensional hopping of Hopf solitons

Arising in many branches of physics, Hopf solitons are three-dimensional particle-like field distortions with nontrivial topology described by the Hopf map. Despite their recent discovery in colloids and liquid crystals, the requirement of applied fields or confinement for stability impedes their utility in technological applications. Here we demonstrate stable Hopf solitons in a liquid crystal material without these requirements as a result of enhanced stability by tuning anisotropy of parameters that describe energetic costs of different gradient components in the molecular alignment field. Nevertheless, electric fields allow for inter-transformation of Hopf solitons between different geometric embodiments, as well as for their three-dimensional hopping-like dynamics in response to electric pulses. Numerical modelling reproduces both the equilibrium structure and topology-preserving out-of-equilibrium evolution of the soliton during switching and motions. Our findings may enable myriads of solitonic condensed matter phases and active matter systems, as well as their technological applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Accurate protein synthesis is determined by the two-subunit ribosome’s capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by antibiotics, remains incompletely understood. Using molecular simulations, we find that cognate and near-cognate tRNAs delivered to the ribosome by Elongation Factor Tu (EF-Tu) can follow divergent pathways of motion into the ribosome during both initial selection and proofreading. Consequently, cognate aa-tRNAs follow pathways aligned with the catalytic GTPase and peptidyltransferase centers of the large subunit, while near-cognate aa-tRNAs follow pathways that are misaligned. These findings suggest that differences in mRNA codon-tRNA anticodon interactions within the small subunit decoding center, where codon-anticodon interactions occur, are geometrically amplified over distance, as a result of this site’s physical separation from the large ribosomal subunit catalytic centers. These insights posit that the physical size of both tRNA and ribosome are key determinants of the tRNA selection fidelity mechanism.

59 BASIC BIOLOGICAL SCIENCES↗

Geometrically frustrated interactions drive structural complexity in amorphous calcium carbonate

Amorphous calcium carbonate is an important precursor for biomineralization in marine organisms. Key outstanding problems include understanding the structure of amorphous calcium carbonate and rationalizing its metastability as an amorphous phase. Here we report high-quality atomistic models of amorphous calcium carbonate generated using state-of-the-art interatomic potentials to help guide fits to X-ray total scattering data. Exploiting a recently developed inversion approach, we extract from these models the effective Ca∙∙∙Ca interaction potential governing the structure. This potential contains minima at two competing distances, corresponding to the two different ways that carbonate ions bridge Ca 2+ -ion pairs. We reveal an unexpected mapping to the Lennard-Jones–Gauss model normally studied in the context of computational soft matter. The empirical model parameters for amorphous calcium carbonate take values known to promote structural complexity. We thus show that both the complex structure and its resilience to crystallization are actually encoded in the geometrically frustrated effective interactions between Ca 2+ ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometrically stabilized skyrmionic vortex in FeGe tetrahedral nanoparticles

The concept of topology has dramatically expanded the research landscape of magnetism, leading to the discovery of numerous magnetic textures with intriguing topological properties. A magnetic skyrmion is an emergent topological magnetic texture with a string-like structure in three dimensions and a disk-like structure in one and two dimensions. Skyrmions in zero dimensions have remained elusive due to challenges from many competing orders. Here, by combining electron holography and micromagnetic simulations, we uncover the real-space magnetic configurations of a skyrmionic vortex structure confined in a B20-type FeGe tetrahedral nanoparticle. An isolated skyrmionic vortex forms at the ground state and this texture shows excellent robustness against temperature without applying a magnetic field. Furthermore, our findings shed light on zero-dimensional geometrical confinement as a route to engineer and manipulate individual skyrmionic metastructures.

36 MATERIALS SCIENCE↗

Interwoven magnetic kagome metal overcomes geometric frustration

Magnetic kagome materials provide a platform for exploring magneto-transport phenomena, symmetry breaking and charge ordering driven by the intricate interplay among electronic structure, topology and magnetism. Yet geometric frustration in conventional kagome magnets limits their tunability. Here we propose a design strategy for interweaving quasi-one-dimensional magnetic Tb zigzag chains with non-magnetic Ti-based kagome bilayers in TbTi 3 Bi 4 . Comprehensive spectroscopic analyses reveal coexisting elliptical-spiral magnetic and spin-density-wave orders accompanied by a large ~90 meV band-folding gap. The combined magnetic and electronic state leads to a giant anomalous Hall conductivity of 10 5 Ω −1 cm −1 , which exceeds that observed in frustrated kagome analogues. These results establish TbTi 3 Bi 4 as a model system of magnetic kagome metals with strong electron–magnetism interactions and underscore the necessity of interweaving designed magnetic and charge layers separately to achieve tunable transport properties. This design strategy will enable the discovery of emergent quantum states and next-generation electronic materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Cuboidal Liquid Crystal Phases Under Multiaxial Geometrical Frustration.

Cuboidal liquid crystal phases - the so-called blue phases - consist of a network of topological defects arranged into a cubic symmetry. They exhibit striking optical properties, including Bragg reflection in the visible range and fast response times. Confining surfaces can interfere with the packing of such a network, leading to structures that have not been explored before. In this work, a Landau-de Gennes free energy formalism for the tensor alignment field Q is used to investigate the behavior of chiral liquid crystals under non-isotropic confinement. The underlying free energy functional is solved by relying on a Monte Carlo method that facilitates efficient exploration of configuration space. The results of simulations are expressed in terms of phase diagrams as a function of chirality and temperature for three families of spheroids: oblate, spherical, and prolate. Upon deformation, blue phases adapt and transform to accommodate the geometrical constraints, thereby resulting in a wider range of thermal stability. For oblate spheroids, confinement interferes with the development of a full blue phase structure, resulting on a combination of half skyrmions. For prolate spheroids, the blue phases are hybridized and exhibit features of blue phases I and II. More generally, it is shown that mechanical deformation provides an effective means to control, manipulate and stabilize blue phases and cholesterics confined in tactoids.

Palacio-Betancur, Viviana↗

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

In many biological systems, the curvature of the surfaces cells live on influences their collective properties. Curvature should likewise influence the behavior of active colloidal particles. We show using molecular simulation of self-propelled active particles on surfaces of Gaussian curvature (both positive and negative) how curvature sign and magnitude can alter the system's collective behavior. Curvature acts as a geometrical lens and shifts the critical density of motility-induced phase separation (MIPS) to lower values for positive curvature and higher values for negative curvature, which we explain theoretically by the nature of parallel lines in spherical and hyperbolic space. Curvature also fluidizes dense MIPS clusters due to the emergence of defect patterns disrupting the crystalline order inside the clusters. Using our findings, we engineer three confining surfaces that strategically combine regions of different curvature to produce a host of novel dynamical behaviors, including cyclic MIPS on spherocylinders, directionally biased cyclic MIPS on spherocones, and position dependent cluster fluctuations on metaballs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-layering of SU-8 exhibits distinct geometrical transitions from circular to planarized profiles

The negative tone photoresist SU-8 permits the creation of micrometer-scale structures by optical lithography. It is also the most used photoresist in soft lithography for the fast-prototyping of microfluidic devices. Despite its importance, the effect of capillary forces on SU-8 multi-layering onto topographical features has not been thoroughly studied. In particular, the profile of the added layer has not been examined in detail. The overlaying process exhibits a set of distinct behaviors, or regimes, depending on the relative thickness of the overlay and the underlying rectangular pattern. We demonstrate how capillary effects control the profile of multi-layer microchannels in a predictable manner. We derive a simple static model to describe the evolution of the overlay as a function of dimensionless geometric parameters. Our study provides a critical understanding of the parameters that govern multi-layer spin coating.

Sauzade, Martin↗

Selecting XFEL single-particle snapshots by geometric machine learning

A promising new route for structural biology is single-particle imaging with an X-ray Free-Electron Laser (XFEL). This method has the advantage that the samples do not require crystallization and can be examined at room temperature. However, high-resolution structures can only be obtained from a sufficiently large number of diffraction patterns of individual molecules, so-called single particles. Here, we present a method that allows for efficient identification of single particles in very large XFEL datasets, operates at low signal levels, and is tolerant to background. This method uses supervised Geometric Machine Learning (GML) to extract low-dimensional feature vectors from a training dataset, fuse test datasets into the feature space of training datasets, and separate the data into binary distributions of “single particles” and “non-single particles.” As a proof of principle, we tested simulated and experimental datasets of the Coliphage PR772 virus. We created a training dataset and classified three types of test datasets: First, a noise-free simulated test dataset, which gave near perfect separation. Second, simulated test datasets that were modified to reflect different levels of photon counts and background noise. These modified datasets were used to quantify the predictive limits of our approach. Third, an experimental dataset collected at the Stanford Linear Accelerator Center. The single-particle identification for this experimental dataset was compared with previously published results and it was found that GML covers a wide photon-count range, outperforming other single-particle identification methods. Moreover, a major advantage of GML is its ability to retrieve single particles in the presence of structural variability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Prediction of chlorine and fluorine crystal structures at high pressure using symmetry driven structure search with geometric constraints

The high-pressure properties of fluorine and chlorine are not yet well understood because both are highly reactive and volatile elements, which have made conducting diamond anvil cell and x-ray diffraction experiments a challenge. Here, we use ab initio methods to search for stable crystal structures of both elements at megabar pressures. We demonstrate how symmetry and geometric constraints can be combined to efficiently generate crystal structures that are composed of diatomic molecules. Furthermore, our algorithm extends the symmetry driven structure search method by adding constraints for the bond length and the number of atoms in a molecule while still maintaining generality. As a method of validation, we have tested our approach for dense hydrogen and reproduced the known molecular structures of Cmca-12 and Cmca-4. We apply our algorithm to study chlorine and fluorine in the pressure range of 10 GPa–4000 GPa while considering crystal structures with up to 40 atoms per unit cell. We predict chlorine to follow the same series of phase transformations as elemental iodine from Cmca to Immm to Fm3¯m, but at substantially higher pressures. We predict fluorine to transition from a C2/c to Cmca structure at 70 GPa, to a novel orthorhombic and metallic structure with P42/mmc symmetry at 2500 GPa, and finally to its cubic analog form with Pm3¯n symmetry at 3000 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗