Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate complex
Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate complex
Cui, Jiawen↗
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Results for “structural complexity”
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Crystal structure of KRED F147L/L153Q/Y190P variant and methyl methacrylate complex
Crystal structure of KRED F147L/L153Q/Y190P variant and methyl methacrylate complex
Cui, Jiawen↗
Variation in Cation Adsorption Mechanism Controlled by Chemical and Structural Heterogeneities at the Quartz (101)–Water Interface
Mineral–water interfacial reactions are central to chemical processes that control the fate of nutrients and contaminants in natural environments. Mineral surfaces commonly have complex structures and compositions whose impact on interfacial reactivity is poorly understood. Here, in this work, we investigated the effects of surface heterogeneities on Rb + sorption at the quartz (101)–10 mM RbCl solution interface at pH 9.8 using in situ high-resolution X-ray reflectivity. Two surface locales (i.e., Spots A and B) having distinct interfacial structures were chosen: Spot A was characterized by its low defect density (≤20% topmost Si vacancies) and Rb + adsorption occurred predominantly as an inner-sphere complex. In comparison, Spot B had a higher defect density (~50% vacancies) and was covered with poorly crystalline SiO 2 . A substantially larger Rb + uptake (i.e., 7-times higher coverage) was observed on this defective surface where Rb + incorporated in the vacancy sites (confirmed by density functional tight binding-based molecular dynamics simulations) or adsorbed directly on the disordered film. These results provide a direct quantification of how surface heterogeneity influences the geochemical behavior of mineral–water interfaces, in particular highlighting the important role of chemical and structural defects on the sorbate speciation and coverage at silicate mineral surfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
In Situ TEM Tensile Testing of Bicrystals with Tailored Misorientation Angles
Grain boundaries have complex structural features that influence strength, ductility and fracture in metals and alloys. Grain boundary misorientation angle has been identified as a key parameter that controls their mechanical behavior, but the effect of misorientation angle has been challenging to isolate in polycrystalline materials. Here, we describe the use of bicrystal Au thin films made using a rapid melt growth process to study deformation at a single grain boundary. Tensile testing is performed on bicrystals with different misorientation angles using in situ TEM, as well as on a single crystalline sample. Plastic deformation is initiated through dislocation nucleation from free surfaces. Grain boundary sliding is not observed, and failure occurs away from the grain boundary through plastic collapse in all cases. The failure behavior in these nanoscale bicrystals does not appear to depend on the misorientation angle or grain boundary energy but instead has a more complex dependence on sample surface structure and dislocation activity.
36 MATERIALS SCIENCE↗
On the structure of the two-stream instability–complex G-Hamiltonian structure and Krein collisions between positive- and negative-action modes
The two-stream instability is probably the most important elementary example of collective instabilities in plasma physics and beam-plasma systems. For a warm plasma with two charged particle species, the instability diagram of the two-stream instability based on a 1D warm-fluid model exhibits an interesting band structure that has not been explained. We show that the band structure for this instability is the consequence of the Hamiltonian nature of the warm two-fluid system. Interestingly, the Hamiltonian nature manifests as a complex G-Hamiltonian structure in wave-number space, which directly determines the instability diagram. Specifically, it is shown that the boundaries between the stable and unstable regions are locations for Krein collisions between eigenmodes with different Krein signatures. In terms of physics, this rigorously implies that the system is destabilized when a positive-action mode resonates with a negative-action mode, and that this is the only mechanism by which the system can be destabilized. It is anticipated that this physical mechanism of destabilization is valid for other collective instabilities in conservative systems in plasma physics, accelerator physics, and fluid dynamics systems, which admit infinite-dimensional Hamiltonian structures.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
One-Dimensional Photonic Crystal Superprisms
Theoretical calculations indicate that it should be possible for one-dimensional (1D) photonic crystals (see figure) to exhibit giant dispersions known as the superprism effect. Previously, three-dimensional (3D) photonic crystal superprisms have demonstrated strong wavelength dispersion - about 500 times that of conventional prisms and diffraction gratings. Unlike diffraction gratings, superprisms do not exhibit zero-order transmission or higher-order diffraction, thereby eliminating cross-talk problems. However, the fabrication of these 3D photonic crystals requires complex electron-beam substrate patterning and multilayer thin-film sputtering processes. The proposed 1D superprism is much simpler in structural complexity and, therefore, easier to design and fabricate. Like their 3D counterparts, the 1D superprisms can exhibit giant dispersions over small spectral bands that can be tailored by judicious structure design and tuned by varying incident beam direction. Potential applications include miniature gas-sensing devices.
Ting, David↗
Forest aboveground biomass estimation through integration of sentinel-2 and PALSAR-2 time series: assessing models trained on GEDI and field inventory benchmarks
Accurate and spatially explicit forest Aboveground Biomass (AGB) mapping through remote sensing is critical for quantifying terrestrial carbon stocks and informing effective forest management strategies. However, AGB estimation in dense forests with complex terrain remains challenging due to satellite sensor signal saturation problem (saturation issue occurs in high biomass forests), structural complexity, and limited ground truth for calibration. This study presents a novel framework that integrates multi-temporal Sentinel-2 optical imagery, ALOS PALSAR-2 Synthetic Aperture Radar (SAR) data, and topographic variables with explainable Machine Learning to map AGB across mountainous forests within subtropical and temperate oceanic climate zones of Mexico. We evaluate the effects of temporal granularity and sensor synergy by comparing multiple temporal inputs and sensor configurations (Sentinel-2, PALSAR-2, and their fusion), and assess model performance using two reference datasets: NASA GEDI LiDAR-derived biomass and Mexico’s National Forest and Soil Inventory (INFyS). Our results showed that models trained on INFyS consistently outperformed those trained on GEDI, highlighting limitations in GEDI’s reliability in biomass estimates within this study region. Furthermore, the integration of Sentinel-2 and PALSAR-2 provided improved predictions compared to single-sensor models, particularly when combined with temporally explicit yearly statistics. The best-performing model, which was trained on INFyS data, and considered both Sentinel-2 and PALSAR-2 yearly statistics, as well as topographic variables, achieved an R2 of 0.64, RMSE of 51.10 Mg/ha, and relative RMSE (rRMSE) of 58.69%. Explainable ML analysis identified Sentinel-2 spectral indices and topographic features as key predictors, while PALSAR-2 metrics provided complementary information, partially mitigating saturation effects in high-biomass areas. Specifically, integrating both sensors substantially improved AGB estimation in high biomass forest (≥200 Mg/ha), yielding 98% gains over optical-only model, with resulting estimates exceeding GEDI L4B by 29% and ESA-CCI-BIOMASS by 174%. Terrain-stratified analysis indicated close agreement with GEDI in low-slope areas, with increasing divergence as slope steepness increased, while estimates remained consistently higher than ESA-CCI-BIOMASS across all slope classes. The proposed approach advances multi-sensor fusion and temporal feature engineering for AGB mapping using open-access satellite datasets, providing a scalable and reproducible framework for annual biomass monitoring in topographically complex mountainous forests. The resulting 25 m resolution biomass product has the potential to provide spatially detailed information for forest monitoring and may support applications in carbon accounting and forest management.
54 ENVIRONMENTAL SCIENCES↗
A cut-cell finite volume – finite element coupling approach for fluid–structure interaction in compressible flow
We present a loosely coupled approach for the solution of fluid–structure interaction problems between a compressible flow and a deformable structure. The method is based on staggered Dirichlet–Neumann partitioning. The interface motion in the Eulerian frame is accounted for by a conservative cut-cell Immersed Boundary method. The present approach enables sub-cell resolution by considering individual cut-elements within a single fluid cell, which guarantees an accurate representation of the time-varying solid interface. The cut-cell procedure inevitably leads to non-matching interfaces, demanding for a special treatment. A Mortar method is chosen in order to obtain a conservative and consistent load transfer. We validate our method by investigating two-dimensional test cases comprising a shock-loaded rigid cylinder and a deformable panel. Moreover, the aeroelastic instability of a thin plate structure is studied with a focus on the prediction of flutter onset. Finally, we propose a three-dimensional fluid–structure interaction test case of a flexible inflated thin shell interacting with a shock wave involving large and complex structural deformations.
42 ENGINEERING↗
Designing the Interface of Carbon Nanotube/Biomaterials for High-Performance Ultra-Broadband Photodetection
Inorganic/biomolecule nanohybrids can combine superior electronic and optical properties of inorganic nanostructures and biomolecules for optoelectronics with performance far surpassing that achievable in conventional materials. The key toward a high-performance inorganic/biomolecule nanohybrid is to design their interface based on the electronic structures of the constituents. A major challenge is the lack of knowledge of most biomolecules due to their complex structures and composition. Here, we first calculated the electronic structure and optical properties of one of the cytochrome c (Cyt c) macromolecules (PDB ID: 1HRC) using ab initio OLCAO method, which was followed by experimental confirmation using ultraviolet photoemission spectroscopy. For the first time, the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels of Cyt c, a well-known electron transport chain in biological systems, were obtained. On the basis of the result, pairing the Cyt c with semiconductor single-wall carbon nanotubes (s-SWCNT) was predicted to have a favorable band alignment and built-in electrical field for exciton dissociation and charge transfer across the s-SWCNT/Cyt c heterojunction interface. Excitingly, photodetectors based on the s-SWCNT/Cyt c heterojunction nanohybrids demonstrated extraordinary ultra-broadband (visible light to infrared) responsivity (46–188 A W –1 ) and figure-of-merit detectivity $D*$ (1–6 × 10 10 cm Hz 1/2 W –1 ). Moreover, these devices can be fabricated on transparent flexible substrates by a low-lost nonvacuum method and are stable in air. These results suggest that the s-SWCNT/biomolecule nanohybrids may be promising for the development of CNT-based ultra-broadband photodetectors.
36 MATERIALS SCIENCE↗
Structural and Interphasial Stabilities of Sulfurized Polyacrylonitrile (SPAN) Cathode
Sulfurized polyacrylonitrile (SPAN) has attracted a lot of attention because of its low cost, high capacity, and great reversibility. Due to its structural complexity and amorphous nature, reaction mechanism of SPAN is little understood. Here, for this paper, we study the structural and interphasial changes of SPAN using synchrotron-based pair distribution function (PDF) analysis and soft X-ray absorption spectroscopy (sXAS). PDF identifies key structural features, including C–S bond, sulfur dimer, and sulfur chain in SPAN. The sulfur dimer bridging the pyridine network partially converts to sulfur chain during the first charging. In the following cycles, sulfur chain goes through lithiation and delithiation with reversibility dependent on the electrolytes. SXAS reveals surface changes of SPAN. After the first cycle, a negatively charged carbon or fused benzene layer is formed, on top of which is another layer formed by the electrolyte decomposition. The layer formed by localized high concentration electrolyte is stable during cycling.
25 ENERGY STORAGE↗
Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry
Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated from the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.
59 BASIC BIOLOGICAL SCIENCES↗
Rapid curing dynamics of PEG-thiol-ene resins allow facile 3D bioprinting and in-air cell-laden microgel fabrication
Thiol-norbornene photoclick hydrogels are highly efficient in tissue engineering applications due to their fast gelation, cytocompatibility, and tunability. In this work, we utilized the advantageous features of polyethylene glycol (PEG)-thiol-ene resins to enable fabrication of complex and heterogeneous tissue scaffolds using 3D bioprinting and in-air drop encapsulation techniques. We demonstrated that photoclickable PEG-thiol-ene resins could be tuned by varying the ratio of PEG-dithiol to PEG norbornene to generate a wide range of mechanical stiffness (0.5–12 kPa) and swelling ratios. Importantly, all formulations maintained a constant, rapid gelation time (<0.5 s). We used this resin in biological projection microstereolithography (BioPµSL) to print complex structures with geometric fidelity and demonstrated biocompatibility by printing cell-laden microgrids. Moreover, the rapid gelling kinetics of this resin permitted high-throughput fabrication of tunable, cell-laden microgels in air using a biological in-air drop encapsulation apparatus (BioIDEA). We demonstrated that these microgels could support cell viability and be assembled into a gradient structure. This PEG-thiol-ene resin, along with BioPµSL and BioIDEA technology, will allow rapid fabrication of complex and heterogeneous tissues that mimic native tissues with cellular and mechanical gradients. The engineered tissue scaffolds with a controlled microscale porosity could be utilized in applications including gradient tissue engineering, biosensing, and in vitro tissue models.
36 MATERIALS SCIENCE↗
Nonlinear Acoustic Response of an Aircraft Fuselage Sidewall Structure by a Reduced-Order Analysis
A reduced-order nonlinear analysis of a structurally complex aircraft fuselage sidewall panel is undertaken to explore issues associated with application of such analyses to practical structures. Of primary interest is the trade-off between computational efficiency and accuracy. An approach to modal basis selection is offered based upon the modal participation in the linear regime. The nonlinear static response to a uniform pressure loading and nonlinear random response to a uniformly distributed acoustic loading are computed. Comparisons of the static response with a nonlinear static solution in physical degrees-of-freedom demonstrate the efficacy of the approach taken for modal basis selection. Changes in the modal participation as a function of static and random loading levels suggest a means for improvement in the basis selection.
Przekop, Adam↗
A Concept for the Deployment of a Large Lunar Crater Radio Telescope Using Teams of Tethered Robots
Kilometer-scale craters on the far side of the Moon have unique potential as future locations for large radio telescopes, which can observe the universe at wavelengths and frequencies (> 10 m, < 30 MHz) not possible with conventional Earth or orbital-based approaches. Distinct advantages of building a Lunar Crater Radio Telescope (LCRT) on the far side include i) isolation from radio noise due to the Earth’s ionosphere, orbiting satellites, and the Sun, ii) days of uninterrupted dark/cold sky viewing during lunar night, and iii) terrain geometry naturally suited for constructing the largest mesh antenna structure in the Solar System. A key challenge to constructing LCRT on the Moon is related to the complexity of deploying a 1-km diameter antenna and hanging receiver within a lunar crater whose diameter, depth, and slope are 3-5 km, 1 km, and ~30 degrees respectively. In this paper, we first evaluate the trade space for deploying a large, complex structure within a crater, and then provide a more detailed concept evaluation of our favored approach, which employs coordinated teams of tethered rovers to extract and suspend a folded antenna from a lander at the base of a crater. NASA’s Jet Propulsion Laboratory in collaboration with California Institute of Technology (Caltech) have developed a novel robotic system for accessing extremely steep terrains; the Axel rover is a two-wheeled rugged terrain vehicle that is supported by an electro-mechanical tether that provides power, data, and tensile support from a top-side anchor location. Recently, a pair of Axel robots have been used in a DuAxel configuration that allows for four-wheel driving and repeated passive anchoring at different locations. The DuAxel system has unique advantages for deploying an LCRT antenna, including the ability to deploy from a lander near a crater, drive a distance to the crater rim to deploy an Axel, and later, retract the deployed Axel in order to sequentially lift up sections of the antenna. Our proposed concept involves delivering a packaged antenna and receiver to the bottom-center of a crater floor on a lander, then later sending a team of multiple DuAxel rovers to retrieve guide wires from the lander, which are pulled to the top of the crater. We explore this concept in detail and provide some initial quantitative analysis to demonstrate the feasibility of our system with respect to the spatial and mass properties of the antenna as juxtaposed to DuAxel capabilities. Finally, we outline next steps towards validating our concept on the way to a future lunar deployment opportunity.
Hallinan, Greg↗
A hydrogen bonded Co(II) coordination complex and a triply interpenetrating 3-D manganese(II) coordination polymer from diaza crown ether with dibenzoate sidearms
In this paper, the diaza crown ether dicarboxylate ligand, 4,4'-((1,7-dioxa-4,10-diazacyclododecane-4,10-diyl)bis(methylene)dibenzoate), L, forms a monomeric coordination complex of Co(II) ions, CoL(H 2 O) 2 ·2H 2 O, 1, and a coordination polymer (MnL·H 2 O) n , 2, with Mn(II) ions under hydrothermal conditions. The monomeric coordination complex (structure 1) is polar with mirror symmetry and crystallizes in the non-centrosymmetric space group Cm. The mirror plane bisects the complex at the six-coordinate Co(II) ion, the two oxygen atoms of the crown moiety and the two oxygen atoms from coordinated water molecules. The coordinated water molecules take part in strong, linear hydrogen bonds with carboxylate oxygens provided by neighboring Co(II)–crown complexes resulting in a three-dimensional (1 : 1) n polar network in which the topology of the underlying 8-coordinated net is sqc3. The structure of 2 crystallizes in the orthorhombic Fdd2 space group as an infinite, polar triply interpenetrating three-dimensional network. The eight-coordinate Mn(II) ion coordinates two oxygen and two nitrogen atoms of the crown moiety, as well as single carboxylate O atom from each of two neighboring ligands. In both structures, the ligand assumes a flexed-wing bird shape, with the two benzoate sidearms of the crown moiety locked in a syn orientation. The metal ion elevated above the plane of the diaza-crown oxygen and nitrogen atoms. The diaza-crown moiety with its two benzoate sidearms has the peculiar property of forming an oriented crystal structure where the metal-crown vectors are oriented parallel to each other in the crystal. However, the structures are achiral, but the rigid crystal lattice prevents re-orientation of the structure through inversion. The coordination polymer (MnL·H 2 O) n , 2, is a 3-center uninodal net with ths (ThSi 2 ) topology. Computational results using the density functional theory (DFT) calculations explain why the flexed-wing bird shape is the preferred and most stable ligand conformation for metal ion binding. Finally, both structures demonstrate magnetic properties that are characteristics of the respective non-interacting isolated paramagnetic transition metal ions that are present.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
THE MORPHOLOGY AND DYNAMICS OF JET-DRIVEN SUPERNOVA REMNANTS: THE CASE OF W49B
The circumstellar medium (CSM) of a massive star is modified by its winds before a supernova (SN) explosion occurs, and thus the evolution of the resulting supernova remnant (SNR) is influenced by both the geometry of the explosion as well as the complex structure of the CSM. Motivated by recent work suggesting the SNR W49B was a jet-driven SN expanding in a complex CSM, we explore how the dynamics and the metal distributions in a jet-driven explosion are modified by the interaction with the surrounding environment. In particular, we perform hydrodynamical calculations to study the dynamics and explosive nucleosynthesis of a jet-driven SN triggered by the collapse of a 25 M {sub ☉} Wolf-Rayet star and its subsequent interaction with the CSM up to several hundred years following the explosion. We find that although the CSM has small-scale effects on the structure of the SNR, the overall morphology and abundance patterns are reflective of the initial asymmetry of the SN explosion. Thus, we predict that jet-driven SNRs, such as W49B, should be identifiable based on morphology and abundance patterns at ages up to several hundred years, even if they expand into a complex CSM environment.
79 ASTRONOMY AND ASTROPHYSICS↗
Structural basis for multiple gene regulation by human DUX4
Highlights: • DUX4 is a master regulator that controls the expression of multiple genes. • DUX4-DH/DNA complex structure was solved at high resolution. • DH1 and DH2 domains of DUX4 play important role in consensus sequence recognition. • DUX4 can tolerate length and/or identity variation in target DNA linker region. DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes. Here we report on the structural and biochemical studies of DUX4 double homeodomains (DUX4-DH), representing the only structures contain both homeodomain 1 (HD1) and homeodomain 2 (HD2). HD1 and HD2 adopt classical homeobox fold; via the helix inserted into the major groove and the N-terminal extended loop inserted into the minor groove, HD1 and HD2 recognize the box1 (5′-TAA-3′) and box2 (5′-TGA-3′) nucleotides of the consensus sequence, respectively. Among the box1 and box2 linking nucleotides (CCTAA), the two adenine residues are reported to be highly conserved; however, they are not directly recognized by DUX4-DH in the structures. Besides different nucleotides, our ITC analysis indicated that DUX4-DH can also tolerate various changes in the linker length. Our studies not only revealed the basis for target DNA recognition by DUX4, but also advanced our understanding on multiple gene activation by DUX4.
60 APPLIED LIFE SCIENCES↗
Molecular Dynamics Calculations
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two winning videos in a competition held at the meeting of the American Physical Society's Division of Fluid Dynamics, held in Atlanta, Georgia, in November 1994. Of great interest was the result that in every shock there were a few high-speed precursor particles racing ahead of the shock, carrying information about its impending arrival. Most recently, Dr. Woo has been applying molecular dynamics techniques to the problem of determining the drag produced by the space station truss structure as it flies through the thin residual atmosphere of low-Earth orbit. This problem is made difficult by the complex structure of the truss and by the extreme supersonic nature of the flow. A fully filled section of the truss has already been examined, and drag predictions have been made. Molecular dynamics techniques promise to make realistic drag calculations possible even for very complex partially filled truss segments flying at arbitrary angles.
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