Search Results (181)

Accurate prediction of protein sidechain conformations is a fundamental challenge in structural biology, with diverse applications ranging from protein structure determination to computational drug design. The performance of backbone-dependent rotamer libraries is often limited by discrete binning artifacts and difficulties handling sparse conformational regions. In this work, we present a Bayesian framework for rotamer prediction that addresses these limitations through Dirichlet priors and spatial smoothing. Our approach models rotamer probabilities as continuous functions of backbone dihedral angles, using circular Gaussian convolution, to make the most of statistical strength from neighboring conformations while respecting the periodic nature of angular data. We constructed rotamer libraries through structural clustering of sidechain conformations rather than chi angle binning, ensuring that each rotamer represents a distinct three-dimensional geometry. We evaluated and compared our framework against the state-of-the-art libraries on two independent test sets. Our Dirichlet model achieved chi angle prediction accuracy of 59–60%. Notably, our method produced consistently lower angular errors, an approximate 13% reduction in mean deviation, suggesting that the continuous probability distributions better capture subtle conformational preferences. Further, we explored the incorporation of non-sequential context by including the identity of nearby non-neighboring residues as an example of extensibility of our framework. Full article

Segmenting CAD models into developable surface patches is a fundamental problem in geometric modeling and manufacturing-oriented applications. Existing approaches often rely on discrete Gaussian curvature estimation or Gauss map analysis; however, their performance on CAD meshes is frequently hindered by numerical instability, sensitivity to mesh tessellation, and complex parameter tuning. In this work, we propose a simple and robust method for developable surface segmentation based on a sparse normal discontinuity prior. Our key observation is that industrial CAD models are typically composed of large developable regions separated by a sparse set of sharp creases and edges. Consequently, segmentation boundaries correspond to sparse discontinuities in the surface normal field rather than continuous variations in curvature. Based on this perspective, we formulate developable surface segmentation as the detection of sparse normal jump discontinuities. In the discrete setting of triangle meshes, this formulation naturally leads to a dihedral angle-based approach that avoids explicit curvature estimation and admits an efficient graph-based solution. The proposed algorithm consists of face normal computation, dihedral angle-based boundary detection, and connected component extraction on a thresholded face adjacency graph. The method requires only a single geometrically interpretable parameter and naturally aligns segmentation boundaries with sharp features commonly found in CAD models. Experimental results on a diverse set of industrial CAD meshes, including standard benchmarks widely used in related research, demonstrate that the proposed approach achieves robust and accurate segmentation, as validated by both visual coherence and quantitative developability metrics. Full article

Iron(II) complexes bearing N-heterocyclic carbene (NHC) ligands have emerged as promising earth-abundant dye sensitizers for applications in dye-sensitized solar cells (DSSCs). In this work, we present a computational study of a set of 42 Fe–NHC dyes derived from seven ligand frameworks, systematically functionalized with donor, acceptor, and donor–acceptor groups to tune or enhance their photophysical properties. The calculated geometries reveal that substitution modulates Fe–N bond lengths and ligand dihedral angles only slightly, preserving the structural integrity of the complexes. TD-DFT calculations show clear and predictable electronic trends: donor groups raise the HOMO, acceptor groups lower the LUMO, and the combined push–pull configuration produces the most pronounced HOMO–LUMO gap narrowing and largest redshifts in MLCT transitions. Key DSSC performance descriptors, including electron-injection and dye-regeneration free energies, light-harvesting efficiency, excited-state lifetimes, and hole-transport reorganization energies, collectively identify the double-acceptor and push–pull derivatives as the most promising candidates across multiple frameworks. Full article

The $\beta$-sheet, consisting of several $\beta$-strands, is one of the most important secondary structures of proteins. Most $\beta$-sheets differ greatly from the fully extended, all-trans form due to twisting and/or bending. When looked at in the direction of the $\beta$-strands rather than along the hydrogen bonds, the twist is usually right-handed. Although numerous studies have investigated the origin of the right-handed twist of $\beta$-sheets or $\beta$-strands in proteins, there is no common agreement about its causes. The twist can be seen from the dihedral angles in the Ramachandran plot. Here, we discuss the opposing roles of the dihedral angles $\varphi$ and $\psi$. The key role is played by the angle $\varphi$, which is controlling the distance between the carbonyl group of the backbone and the side chain of the next amino acid. There are two antisymmetric effects: the change in $\varphi$ in the clockwise direction is initiated by a ${\mathrm{C}}_{\beta }$… O clash and delimited by a subsequent ${\mathrm{C}}_{\beta }$… NH clash, while the opposite relationship holds for the counter-clockwise change in $\psi$. The impact of the twist on tertiary structures is examined. The understanding of the molecular effects within a strand is deepened by 3D computer images and ball–and–stick models. The use of (tangible) physical models is highlighted in view of teaching structural biology to undergraduate students. Full article

The photophysical properties of a BODIPY derivative with the highly twisted molecular structure of anthracene-fused boron–dipyrromethene (AN-BDP) were studied with steady-state and time-resolved spectroscopic methods. The fused anthryl and the BDP units in AN-BDP units both adopt distorted geometry (with ca. 10° of torsion), and there is large dihedral angle between the two units (ca. 49.7°). Interestingly, the fluorescence quantum yields are highly dependent on the solvent polarity (59~3%, from toluene to acetonitrile), yet the fluorescence emission wavelength does not change in different solvents. Nanosecond transient absorption spectra indicate that the triplet state is long-lived, with an intrinsic triplet state lifetime of 551 μs. Interestingly the severely twisted structure only shows a moderate intersystem crossing (ISC) yield (10%). Femtosecond transient absorption spectra indicate slow ISC (>1.5 ns), which is in agreement with the fluorescence lifetime (2.3 ns). Time-resolved electron paramagnetic resonance (TREPR) spectra show smaller zero-field-splitting D and E tensors as (−71.4 mT, 16.7 mT, respectively) compared to the triplet state of the iodinated native BDP (D = −104.6 mT, E = 22.8 mT), inferring that the triplet-state wave function of the new compound is delocalized over the twisted molecular framework. The theoretical computation indicated a solvent-polarity-dependent energy barrier for the relaxed S₁ state to a conical interaction (CI) of the S₁ and the S₀ state potential curves, which agrees with the weaker fluorescence in polar solvents. Full article

The conformation of a glycosaminoglycan (GAG) carbohydrate biopolymer is dependent upon the ring puckering states of its constituent monosaccharide residues and the dihedral angles (φ, ψ) of the glycosidic linkages connecting these residues. In the context of GAGs, the monosaccharide residue iduronate (IdoA; the conjugate base of iduronic acid) is able to take on both chair and boat-like ring pucker states. All-atom explicit-solvent molecular dynamics simulations were applied to determine the extent to which IdoA ring pucker state affects the conformational preferences of (φ, ψ) in 16 different IdoA-containing disaccharides derived from the GAGs heparin/heparan sulfate and dermatan sulfate. Using the extended-system adaptive biasing force (eABF) method, the complete free-energy surface ΔG(φ, ψ) was computed for each disaccharide with its IdoA ring restrained separately to the ¹C₄, ²S_O, B_3,O, or ⁴C₁ ring pucker state. Global-minimum ΔG(φ, ψ) values resided within broad ΔG(φ, ψ) basins, and both ring pucker state and sulfation status influenced basin shape and size. Various sulfoforms of the disaccharide IdoAα1–4GlcNS had prominent secondary-minimum basins distinct from the global-minimum basins, and these secondary-minimum basins may manifest as metastable states in standard (nonbiased) molecular dynamics simulations on the 1-microsecond timescale. As such, the present results provide a reference for assessing (φ, ψ) sampling in nonbiased molecular dynamics simulations of GAGs and demonstrate the interplay between IdoA ring puckering, glycosidic linkage dihedral rotation, and sulfation status in contributing to GAG conformational preferences. Full article

The aerodynamic performance of unmanned aerial vehicles (UAVs) with non-conventional geometries is a growing area of interest, particularly for improving stability and maneuverability. This study investigates the influence of the dihedral angle on the aerodynamic behavior and overall performance of drones configured in an X-wing layout. Four configurations with dihedral angles of 0°, 15°, 30°, and 45° were analyzed to assess how varying the wing inclination affects flight characteristics. Computational fluid dynamics (CFD) simulations were conducted to evaluate the aerodynamic forces and moments acting on each configuration under controlled conditions. Following the aerodynamic analysis, a performance assessment was carried out to determine the implications of each dihedral angle on parameters such as range, endurance, rate of climb, angle of climb or turn rate. The results indicate that increasing the dihedral angle can enhance maneuverability but may lead to trade-offs in aerodynamic efficiency, particularly at higher angles. The 15° and 30° configurations demonstrated a favorable balance between maneuverability and performance. These findings provide insight into the design optimization of X-wing UAVs and highlight the potential of dihedral angle tuning as a means to tailor drone behavior for specific operational needs. Full article

Accurate interpretation of missense variants in cancer-associated genes remains a critical challenge in precision oncology, as most sequence-based predictors lack mechanistic explanations. Receptor tyrosine kinases like FGFR2 exemplify this problem: their function depends on conformational dynamics, yet most variants remain classified as variants of uncertain significance (VUS). In this paper we present DyVarMap, an interpretable structural-learning framework that integrates AlphaFold2-based ensemble generation with physics-driven refinement, manifold learning, and supervised classification using five biophysically motivated geometric features. Applied to FGFR2, the framework generates diverse conformational ensembles, identifies metastable states through nonlinear dimensionality reduction, and classifies pathogenicity while providing mechanistic attributions via SHAP analysis. External validation on ten kinase-domain variants yields an AUROC of 0.77 with superior calibration (Brier score = 0.108) compared to PolyPhen-2 (0.125) and AlphaMissense (0.132). Feature importance analysis consistently identifies K659–E565 salt-bridge distance and DFG motif dihedral angles as top predictors, directly linking predictions to known activation mechanisms. Case studies of borderline variants (A628T, E608K, L618F) demonstrate the framework’s ability to provide structurally coherent mechanistic explanations. DyVarMap bridges the gap between static structure prediction and dynamics-aware functional assessment, generating testable hypotheses for experimental validation and demonstrating the value of incorporating conformational dynamics into variant effect prediction for precision oncology. Full article

ORF8 is the second most mutated protein in SARS-CoV-2. It can form oligomers such as trimers and can bind to the IL-17RA/RC receptor. To understand the possible role of ORF8 in SARS-CoV-2, the first step of this study involved predicting the ORF8 trimer structure and the complex structure of the ORF8 monomer bound to the IL-17RA receptor using docking and molecular dynamics simulation methods. It was found that ORF8 molecules bound to the central ORF8 molecule through covalent and noncovalent interactions exhibit similar RMSD and RMSF values as the central ORF8 molecule and form a similar buried surface area, but display different numbers of hydrogen bonds and varying dynamic correlations. Additionally, trimer formation increases the dynamic correlation of the noncovalently bound ORF8 unit. ORF8 can bind with the IL-17RA receptor stably. Regions on ORF8, including C25–I47, L60–S67, T80–C90, and S103–E110, and regions on IL-17RA, including L1–H63 and D122–M165, are involved in the binding interface of the complex. ORF8 becomes less rigid when bound to IL-17RA than in its monomer, dimer, and trimer forms. Based on dihedral angle correlation predictions, binding of ORF8 to IL-17RA reduces internal correlations within ORF8 while strengthening correlations within IL-17RA. The G50–T80 region of ORF8 appears to be critical for interaction with IL-17RA, and the L1–V150 region of IL-17RA should be critical for its dynamics once bound to ORF8. These results help elucidate the structure and dynamics of ORF8 in SARS-CoV-2. Full article

Designing the high-performance polyimides (PIs) for the biomimetic structures, which are used in extreme conditions, remains greatly challenging, due to the conflict between processability and thermal stability. Here, we report a series of silicon–alkyne-functionalized diamine-based polyimides that exhibit remarkable processability and thermal stability. The incorporation of bulky siloxy groups disrupts chain packing and increases free volume, enabling excellent solubility in polar solvents, while the rigid fluorene core enhances chain stiffness. DFT calculations confirm twisted molecular geometries (Si bond angle ≈ 103°, dihedral angle ≈ 89°) which weak π–π stacking, while heterogeneous electrostatic potentials enable favorable noncovalent interactions (e.g., C–F···H–C), promoting solvent diffusion. After thermal curing, the obtained product shows a high decomposition temperature (T_d5% = 560 °C), char yield of 72.0% at 800 °C, and glass transition temperature (T_g) of 354.6 °C. Meanwhile, locally planar fluorene units retain inherent thermal stabilization benefits through constrained rotational mobility. These results demonstrate a spatially decoupled siloxy–alkyne design that synergistically enhances molecular flexibility, disorder, and electronic stability, offering a molecular strategy for tailoring PI-based matrices to meet the demands of emerging biomimetic architectures and other high-performance composites operating under severe thermal loads. Full article

Silica-rich dust intrusion is a persistent challenge for lubrication systems in agricultural machinery, where abrasive third-body particles can accelerate wear and shorten component service life. Here, molecular dynamics simulations are employed to elucidate how SiO₂ nanoparticle contamination degrades polyalphaolefin (PAO) boundary lubrication at the atomic scale. Two confined sliding models are compared: a pure PAO film and a contaminated PAO film containing 7 wt% SiO₂ nanoparticles between crystalline Fe substrates under a constant normal load and sliding velocity. The contaminated system exhibits a higher steady-state friction force, faster lubricant film disruption and migration, and consistently higher interfacial temperatures, indicating intensified energy dissipation. Substrate analyses reveal deeper and stronger von Mises stress penetration, increased severe plastic shear strain, elevated Fe potential energy associated with defect accumulation, and reduced structural order. Meanwhile, PAO molecules store more intramolecular deformation energy (bond, angle, and dihedral terms), reflecting stress concentration and disturbed shear alignment induced by nanoparticles. These results clarify the multi-pathway mechanisms by which abrasive SiO₂ contaminants transform PAO from a protective boundary film into an agent promoting abrasive wear, providing insights for designing wear-resistant lubricants and improved filtration strategies for particle-laden applications. Full article

This paper proposes a compact polarimetric CTLR mode calibration method using only two dihedral reflectors. The method leverages the property that the dihedral scattering matrix is unaffected by double-pass Faraday rotation, effectively eliminating the interference of Faraday rotation on distortion parameter estimation. By selecting any two from four dihedral reflectors rotated at 0°, 22.5°, 45°, and 67.5°, the system distortion parameters can be estimated. To resolve the two-fold solution ambiguity inherent in the estimation process, two ambiguity elimination methods are proposed: Method I selects the solution with equivalent crosstalk magnitude less than 0 dB based on the prior knowledge that the transmit antenna is dominated by right-hand circular polarization; Method II employs cross-validation using different dihedral combinations with distinct product constants, applicable when the prior knowledge does not hold. Through simulation analysis, the algorithm’s sensitivity to receive crosstalk levels, signal-to-noise ratio, and polarization orientation angle shift is evaluated. The results demonstrate that to maintain residual receive imbalance amplitude within ±1 dB, phase within ±10°, and residual equivalent crosstalk below −30 dB, the system received crosstalk must be lower than −25 dB, the signal-to-noise ratio must exceed 35 dB, and polarization orientation angle shift should be controlled within ±1°. The effectiveness of the proposed algorithm is validated using fully polarimetric calibrated GaoFen-3 satellite data, achieving root mean square errors of 0.10 dB, 1.13°, and 0.42 dB for amplitude imbalance, phase imbalance, and equivalent crosstalk amplitude, respectively. Comparative analysis demonstrates that the proposed method achieves significantly higher calibration accuracy than existing approaches, with substantial improvements in parameter estimation precision. Full article

Auxetic textiles, characterized by a negative Poisson’s ratio, offer considerable promise for innovative applications across multiple fields. In our earlier work, Miura-ori-inspired auxetic fabrics with three different initial dihedral fold angles—30°, 45°, and 60°—were successfully fabricated via jacquard weaving. Their fundamental auxetic behaviors were evaluated, showing deformation characteristics consistent with those in their geometric models. This study further investigates the mechanical properties of Miura-ori-based auxetic woven fabrics. Tensile testing, air permeability measurement, compression performance assessment, and repeated-loading cyclic rope-stretching tests were performed on the three fabric variants. The results show that the fabrics exhibit excellent air permeability, which increases with the proportion of the folded areas; the highest air permeability was observed at Miura-30°. Moreover, Miura-60° exhibited superior compression resistance. The fabrics also demonstrated outstanding structural stability under cyclic tensile loading, exhibiting optimal elastic recovery at the 30° configuration. Collectively, these findings provide a solid theoretical basis for future applications of Miura-ori auxetic woven fabrics. Full article

Flapping-wing micro-air vehicles (FWMAVs) exhibit unique aerodynamic characteristics that differ fundamentally from other aircraft, yet little is known about their dynamic stability derivatives. This study aims to identify pitch-rate stability derivatives of an in-house prototype, CKopter-1, to advance the modeling and control of bio-inspired flight. Experiments were conducted using a robotic-arm fan-array system that enabled prescribed pitching motions under controlled inflow. Aerodynamic forces and moments were measured with a six-axis load cell, while vehicle kinematics were captured using motion tracking and synchronized during post-processing. Tests consisted of quasi-static cycles and dynamic cycles at pitch rates of 35°/s, 58.8°/s, and 68.4°/s. The results revealed static instability below an angle of attack of 33°, a trim condition near 58.5°, and positive stability up to 72.5°. Dynamic cases showed clear pitch-rate effects in the longitudinal components, from which the derivatives were extracted. A comparison with previous studies confirmed comparable magnitudes, with systematic differences attributable to wing dihedral and tail length. This study demonstrates that the fan-array robotic-arm method enables stability derivative identification even beyond feasible flight regimes, providing valuable parameters for future flight dynamics modeling and control of FWMAVs. Full article

Right-angle dihedral structures produce strong, highly correlated returns that dominate radar cross-section (RCS) and image signatures. Conventional absorbers or random coding metasurfaces often lose effectiveness across wide frequency bands and angles, and cannot adequately suppress the corner-induced hot spots. We propose a wideband super-dispersion encoded surface (SDES) conformally applied to dihedral facets. The approach co-designs input-admittance for absorption with a deterministic super-dispersion phase sequence to redistribute energy spectrally and angularly, thereby decorrelating the returns. We implement SDES on a thin composite panel and evaluate it on canonical dihedral and dihedral–cylindrical hybrid configurations. Unlike diffuse or random coding schemes, SDES enforces broadband, angle-stable dispersion with a deterministic sequence that specifically addresses corner singularity scattering. We also introduce perceptual-hashing as an imaging-domain metric to link RCS control with observable radar-image changes. From 12–18 GHz, SDES reduces the average monostatic RCS by 9.6 dB on a right-angle dihedral. In dihedral–cylindrical hybrids, SDES removes the corner hot spots and drives the radar-image similarity index down to 0.31, confirming substantial alteration of scattering signatures. Full article