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Journal articles on the topic 'Dihedral angle control'
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Kinuta, Takafumi, Nobuo Tajima, Michiya Fujiki, Mitsuo Miyazawa, and Yoshitane Imai. "Control of circularly polarized photoluminescent property via dihedral angle of binaphthyl derivatives." Tetrahedron 68, no. 24 (2012): 4791–96. http://dx.doi.org/10.1016/j.tet.2012.03.119.
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Nicy and David J. Wales. "Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides." International Journal of Molecular Sciences 24, no. 13 (2023): 10613. http://dx.doi.org/10.3390/ijms241310613.
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Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.
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Pan, Tianyu, Kaikai Shi, Hanan Lu, Zhiping Li, and Jian Zhang. "Numerical Investigations of a Non-Uniform Stator Dihedral Design Strategy for a Boundary Layer Ingestion (BLI) Fan." Energies 15, no. 16 (2022): 5791. http://dx.doi.org/10.3390/en15165791.
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A distributed propulsion system has the advantage of saving 5–15% fuel burn through ingesting the fuselage boundary layer of an aircraft by fan or compressor. However, due to boundary layer ingestion (BLI), the fan stage will continuously operate under serious inlet distortion. This will lead to a circumferentially non-uniform flow separation distribution on the stator blade suction surface along the annulus, which significantly decreases the fan’s adiabatic efficiency. To solve this problem, a non-uniform stator dihedral design strategy has been developed to explore its potential of improving BLI fan performance. First, the stator full-annulus blade passages were divided into blade dihedral design regions and baseline design regions on the basis of the additional aerodynamic loss distributions caused by BLI inlet distortion. Then, to find the appropriate dihedral design parameters, the full-annulus BLI fan was discretized into several portions according to the rotor blade number and the dihedral design parameter investigations for dihedral depth and dihedral angle were conducted at the portion with the largest inflow distortion through a single-blade-passage computational model. The optimal combinational dihedral design parameter (dihedral depth 0.3, dihedral angle 6 deg) was applied to the blade passages with notable flow loss which were mainly located in the annulus positions from −120 to 60 degrees suffering from inlet distortion, while the blades in the low-loss annulus locations were unchanged. In this way, a non-uniform stator dihedral design scheme was achieved. In the end, the effectiveness of the non-uniform stator dihedral design was validated by analyzing the internal flow fields of the BLI fan. The results show that the stator dihedral design in distorted regions can increase the inlet axial velocity and reduce the aerodynamic load near the blade trailing edge, which are beneficial for suppressing the flow separations and reducing aerodynamic loss. Specifically, compared with the baseline design, the non-uniform stator dihedral design has achieved a reduction of aerodynamic loss of about 7.7%. The fan stage has presented an improvement of adiabatic efficiency of about 0.48% at the redesigned point without sacrificing the total pressure ratio. In the entire operating range, the redesigned fan has also shown a higher adiabatic efficiency than the baseline design with no reduction of the total pressure ratio, which provides a probable guideline for future BLI distortion-tolerant fan design.
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Mori, Hatsumi, Naoki Sakurai, Shoji Tanaka та ін. "Control of Electronic State by Dihedral Angle in θ-type Bis(ethylenedithio)tetraselenafulvalene Salts". Chemistry of Materials 12, № 10 (2000): 2984–87. http://dx.doi.org/10.1021/cm000321+.
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Yoshida, Naoya, Tomoya Ishizuka, Atsuhiro Osuka, et al. "Fine Tuning of Photophysical Properties of mesomeso-Linked ZnII–Diporphyrins by Dihedral Angle Control." Chemistry - A European Journal 9, no. 1 (2003): 58–75. http://dx.doi.org/10.1002/chem.200390004.
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Li, Peilin. "Analysis of Combination of Four, Five Six Crease Vertices Waterbomb." Highlights in Science, Engineering and Technology 18 (November 13, 2022): 59–66. http://dx.doi.org/10.54097/hset.v18i.2569.
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Origami combination is reliable because of great stabilization and controllable deployable. Potential and extensive applied in medical field, as a soft robot gripper. To investigate a possible stabilization structure, this design contained a combination of three four-crease vertexes, one five-crease vertex and one six-crease vertex. The design theory is based on waterbomb pattern design and obey the two design principles. The degree of freedom in this combination would be proof is zero, which demonstrates an over-constrained structure, and also the poor control performance and reliability. The reason might be the compelling in five-crease vertex and multiple Dof in the four-crease vertexes (which might be one Dof), which cause the overall outputs dihedral angles could not be controlled by overall inputs. Additionally, this design has faster equilibrium state because of smaller dihedral angle (smaller than 90 degrees) in each vertex, as an overstrained structure. The future improvement might be done by reduce the Dof in the four-crease vertex and promotion in five-crease vertex.
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Byakova, A. V., YU V. Milman, and A. A. Vlasov. "Application of the plasticity characteristic determined by the indentation technique for evaluation of mechanical properties of coatings: II. guidelines to coating development and processing control." Science of Sintering 36, no. 2 (2004): 93–103. http://dx.doi.org/10.2298/sos0402093b.
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The equilibrium between solid and 1iquid phases in sintered composite materials has been studied. It is shown that closed surfaces, which bound dispersed phases, influence the mechanical equilibrium between these phases. An expression is derived for a dihedral angle in composite materials, which includes values of surface tensions at the phase interfaces as well as parameters of a composite equilibrium structure (phase composition, particle contiguity and coefficients of a particle geometry). .
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Yoshida, Naoya, and Atsuhiro Osuka. "Control of Dihedral Angle of Meso−Meso Linked Diporphyrins by Introducing Dioxymethylene Straps of Various Length." Organic Letters 2, no. 19 (2000): 2963–66. http://dx.doi.org/10.1021/ol006216n.
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Ahn, Tae Kyu, Kil Suk Kim, Deok Yun Kim та ін. "Relationship between Two-Photon Absorption and the π-Conjugation Pathway in Porphyrin Arrays through Dihedral Angle Control". Journal of the American Chemical Society 128, № 5 (2006): 1700–1704. http://dx.doi.org/10.1021/ja056773a.
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Dharmapurikar, Satej S., Sundaresan Chithiravel, Manoj V. Mane, Gunvant Deshmukh, and Kothandam Krishnamoorthy. "Dihedral angle control to improve the charge transport properties of conjugated polymers in organic field effect transistors." Chemical Physics Letters 695 (March 2018): 51–58. http://dx.doi.org/10.1016/j.cplett.2018.01.052.
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Gatto, A., P. Bourdin, and M. I. Friswell. "Experimental Investigation into the Control and Load Alleviation Capabilities of Articulated Winglets." International Journal of Aerospace Engineering 2012 (2012): 1–15. http://dx.doi.org/10.1155/2012/789501.
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An experimental investigation into the real-time flow and control characteristics of a flying wing with articulated winglets is described in this paper. The philosophy of the concept centres around the use of active, in-flight adjustment of each wing's winglet dihedral angle, both as a primary means of aircraft roll control (single winglet actuation) and though smaller equal and simultaneous winglet deflections, tailor and alleviate main wing load. Results presented in this paper do provide good evidence of the concept's ability to adequately perform both tasks, although for the current chosen wing/winglet configuration, roll control authority was unable to achieve, per unit of control surface deflection, the same level of performance set by modern aileron-based roll control methodologies.
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Syamsuar, Sayuti. "Simulasi dan Verifikasi Prestasi Terbang Model Remote Control Flying Boat Saat Hidroplaning." WARTA ARDHIA 42, no. 1 (2017): 1. http://dx.doi.org/10.25104/wa.v42i1.294.1-6.
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Pesawat Wing In Surface Effect A2B tipe B konfigurasi Lippisch mempunyai hambatan air yang cukup besar dibandingkan tenaga mesin saat hydroplaning. Makalah ini berisikan bagian dari analisis dalam perancangan untuk mengetahui karakteristik aerodinamika dan hidrodinamika dari remote control model jenis Flying Boat pada fase hydroplaning. Pada awalnya, dilakukan pemotretan 3D terhadap pesawat model Flying Boat menggunakan kamera laser untuk menghasilkan solid drawing pada program CATIA. Model 3D dianalisis dengan menggunakan piranti lunak CFx pada program AnSys. Planform sayap, memiliki dihedral dan menggunakan airfoil jenis NACA 23012. Karakteristik aerodinamika dan hidrodinamika untuk model 3 D dipresentasikan pada posisi sudut alpha =00. Sedangkan kecepatan yang digunakan adalah 0 sampai25 knots. Untuk memverifikasi data hasil simulasi, digunakan data uji terbang pesawat udara tanpa awak Alap-alap yang mempunyai T/W rasio yang sama, yaitu sudut pitch, kecepatan arah sumbu Z pada sumbu benda, ketinggian dan kecepatan. Gaya angkat aerodimaka arah sumbu Z pada simulasi RC model Flying Boat sebanding dengan gaya angkat aerodinamika arah sumbu Z pada UAV Alap-alap saat take off.
 [The Hydroplaning Flight Performance Simulation and Verfication of a Flying Boat Remote Control Model] The Wing in Surface Effect Aircraft A2B type B with Lippisch configuration has higher hydrodynamics drag compared to engine powered aircraft during hydroplaning. This paper explains parts of analysis in aircraft design to identify the aerodynamics and hydrodynamics characteristics of flying boat remote control model during hydroplaning phase. At first, flying boat model was three dimensional photographed using laser camera in order to produce solid drawing for CATIA program. The three dimensional model, later, analyzed by using CFx software in AnSys program. The wing planform has dihedral angle while the airfoil used is NACA 23012. The aerodynamics and hydrodynamics characteristics of this three-dimensional model is represented for alpha =00. Whilst the speed used in simulation was 0 to 25 knots. In verifying the data of the simulation results, the Unmanned Aerial Vehicle UAV Alap-alap flight test data was used in which it has the same T/W ratio for the pitch angle, acceleration in Z body axis, altitude, and speed. The aerodynamics lift in Z axis of flying boat model during simulation is proportional to the aerodynamics lift in Z axis of UAV Alap-alap during take-off.
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Bourdin, P., A. Gatto, and M. I. Friswell. "Performing co-ordinated turns with articulated wing-tips as multi-axis control effectors." Aeronautical Journal 114, no. 1151 (2010): 35–47. http://dx.doi.org/10.1017/s0001924000003511.
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Abstract This paper investigates a novel method for the control of aircraft. The concept consists of articulated split wing-tips, independently actuated and mounted on a baseline flying wing. The general philosophy behind the concept was that adequate control of a flying wing about its three axes could be obtained through local modifications of the dihedral angle at the wing-tips, thus providing an alternative to conventional control effectors such as elevons and drag rudders. Preliminary computations with a vortex lattice model and subsequent wind tunnel tests and Navier-Stokes computations demonstrate the viability of the concept for co-ordinated turns, with individual and/or combined wing-tip deflections producing multi-axis, coupled control moments. The multi-axis nature of the generated moments tends to over-actuate the flight control system, leading to some redundancy, which could be exploited to optimise secondary objective functions such as drag or bending moment.
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Oh, Chan Seok, Daniel de Sa Pereira, Si Hyun Han, et al. "Dihedral Angle Control of Blue Thermally Activated Delayed Fluorescent Emitters through Donor Substitution Position for Efficient Reverse Intersystem Crossing." ACS Applied Materials & Interfaces 10, no. 41 (2018): 35420–29. http://dx.doi.org/10.1021/acsami.8b10595.
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Then, Li Yee, Huey Chong Kwong, Ching Kheng Quah, et al. "Tyrosinase inhibition potency of phthalimide derivatives: crystal structure, Hirshfeld surface analysis and molecular docking studies." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 11 (2018): 803–16. http://dx.doi.org/10.1515/zkri-2018-2090.
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Abstract A new series of seven 2-((pyridinylamino)methyl)isoindoline-1,3-dione derivatives were synthesized under mild condition and characterized by spectroscopy analysis. The crystal structures of these derivatives were further determined using single crystal X-ray diffraction technique. All derivatives adopt a V-shape conformation. The dihedral angle between phthalimide and pyridine rings increases as the torsion angle C1–N1–C9–N2 between phthalimide ring and methylene group increases. The torsion angles and molecular conformations are comparable to those related structures from the Cambridge Structural Database (CSD). Furthermore, the intermolecular interactions of all studied crystal structures were quantified and analyzed using Hirshfeld surface (HS) analysis. The quantitative data on the percentage contributions of overall interactions in all compounds are calculated by the two-dimensional (2D) fingerprint plots from the HS analysis. These compounds were evaluated for their antioxidant and antityrosinase properties. Noteworthy, 2-(((6-methoxypyridin-3-yl)amino)methyl)isoindoline-1,3-dione (compound g) exhibited higher tyrosinase inhibitory activity (EC50=753 μg/mL) than the positive control ‘arbutin’ (EC50=403 μg/mL). The inhibitory effect of compound g was further confirmed by computational molecular docking studies and the result revealed the 6-methoxypyridin-3-yl substituent has a better binding affinity toward tyrosinase.
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Delannay, Francis. "The role of dihedral angle on the control of skeleton coordination and pore closure in aggregates driven by capillary forces." Scripta Materialia 62, no. 12 (2010): 928–33. http://dx.doi.org/10.1016/j.scriptamat.2010.02.026.
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Arisha, Anan. "Geometrical Optimization and Natural Bond Orbital Analysis of Relevant Structures in the Diastereoselective Cuprate Conjugate Addition Reaction of α,β-Unsaturated Lactams using Density Functional Theory". Asian Journal of Chemistry 35, № 12 (2023): 3071–80. http://dx.doi.org/10.14233/ajchem.2023.30725.
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In this study, density functional theory calculations at the wB97XD/Def2TZVPP level were performed to analyze the mechanism underlying the cuprate conjugate addition reaction of α,β-unsaturated lactams. The calculation results were well-aligned with those obtained experimentally–the keto-aminal and aldo-aminal, i.e. 2 and 1a, yield the syn- and anti-products, respectively. The diastereoselectivity reversal originates from the small differences in the structure of the reactants. The pyramidalization and C7N3C2 angle between the aminal carbon, nitrogen and carbonyl carbon are large in 2. The dihedral angle of the aminal oxygen, aminal carbon, nitrogen and carbonyl carbon, O8C7N3C2, is closer to 180º in 2 than in 1a. The NBO analysis revealed string interactions between the lone pair of N3 and carbonyl π*(O1–C2) bond. These results validate the assumption—the planarity around nitrogen in molecule 2 increases the nucleophilicity of the carbonyl oxygen, thereby driving the reaction between molecule 2 and trimethylsilyl chloride (TMSCl), which yields a siloxyiminium cation 5b and this 5b propels the syn addition of dimethylcuprate, leading to the formation of complex 7. The π(C5–C6) (HOMO) and π*(C2–N3) (LUMO) interactions in the siloxyiminium cation explain the increased C5–C6 double bond electrophilicity. The aldo-aminal 1a directly reacts with dimethylcuprate under steric control and yields the anti complex 6a, whose π character is stronger than that of the syn complex 7 and this weak π characteristics of 7 increases its stability to compensate for the trimethylsilyl disturbance. The bicyclic α,β-unsaturated lactam 8 does not contain aminal oxygen and thus remains unreactive during the cuprate conjugate addition reaction. Moreover, its pyramidalization is higher than that of the keto-aminal 2 and its dihedral angle of C8C7N3C2 is closer to 180º. Finally, a thermodynamic anti product is obtained, which is more stable than the syn- product because of less torsional strain.
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Chen, Xiao Jie. "Study on Wing Layout Design of Aircraft." Applied Mechanics and Materials 178-181 (May 2012): 2881–84. http://dx.doi.org/10.4028/www.scientific.net/amm.178-181.2881.
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This paper describes how the wing surfaces are defined by aerodynamic, stability/control, layout and structural requirements. The size of the wing (area) will usually be dictated by aircraft performance requirements(e.g. field length) but the shape of the planform and other geometry may be influenced by wing layout factors. In the early design stages choices need to be made on the position of the wing relative to the fuselage (e.g. high, mid or low position) and then on the overall envelope. This will include selection of aspect ratio, taper ratio, sweepback angle, thickness ratio and section profile, and dihedral. Each of these decisions is explained. A brief introduction on flap design of the aerodynamic (lift and drag) characteristics of flaps are also described, which is added to explain the wing layout of aircraft.
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Elicer Cortés, J. C., and Doan-Kim Son. "TURBULENT NATURAL CONVECTION IN A DIHEDRAL CAVITY: INFLUENCE OF THE ANGLE AND THE TEMPERATURE OF THE WALLS ON THE MEAN THERMAL FIELD." Experimental Heat Transfer 6, no. 3 (1993): 205–13. http://dx.doi.org/10.1080/08916159308946454.
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Sekine, Akiko, Yuta Yamazaki, Kohei Johmoto, and Hidehiro Uekusa. "Control of Photochromism in Crystalline-State in Dual Photoisomeric Complexes." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C920. http://dx.doi.org/10.1107/s2053273314090792.
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Photochromic materials have attracted attention in recent years, however, in situ control of the photochromic reactivities still challenging. In order to realize dynamic control of photochromic property in crystal, we designed and created new dual photoisomeric type cobaloxime complexes, in which the reactivity of photochromic ligand changes by contact with surrounding photoreactive ligands. In this study, salicylideneaniline derivatives (SAP) are used as photochromic ligands, and the relationships between their photochromic reactivity and structural changes induced by crystalline-state photoisomerization of alkyl group of cobaloxime complex were investigated. As a salicylideneaniline (SAP) type cobaloxime complex, (3-cyanopropyl)(N-(3,5-di-tert-butylsalicylidene)-3-aminopyridine)cobaloxime was successfully synthesized. In the crystal, the SAP moiety which had a twisted conformation (dihedral angle of rings, 30.0(6)0)showed the photochromism upon UV irradiation. Also the 3-1 photoisomerization of the 3-cyanopropyl group in the cobaloxime moiety occurred with retention of the single-crystal form upon visible light irradiation. After crystalline-state 3-1 photoisomerization of the alkyl group by visible light, the photochromic property was examined to show the lifetime of colored species became significantly longer than before the reaction. It would be explained that the reaction cavity around the SAP moiety was modified by solid-state photoisomerization of alkyl group of the surrounding cobaloxime complexes, which successfully enabled the control of the photochromism. Moreover, other several derivatives are investigated similarly and their results were discussed together.
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Qin, Yao-Guo, Zhao-Kai Yang, Jia Fan, Xin Jiang, Xin-Ling Yang, and Ju-Lian Chen. "Synthesis, Crystal Structure and Bioactivities of N-(5-(4-chlorobenzyl)-1,3,5-Triazinan-2-Ylidene)Nitramide." Crystals 10, no. 4 (2020): 245. http://dx.doi.org/10.3390/cryst10040245.
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The compound N-(5-(4-chlorobenzyl)-1,3,5-triazinan-2-ylidene)nitramide (C10H12ClN5O2, M = 269.70) was synthesized and structurally confirmed by 1H NMR, 13C NMR, HRMS and single-crystal x-ray diffraction. The crystal belongs to the monoclinic system with space group P21/c. The title compound consisted of a benzene ring and a 1,3,5-triazine ring. All carbon atoms in the benzene ring were nearly coplanar with a dihedral (C6–C5–C10 and C7–C8–C9) angle of 1.71°and all non-hydrogen atoms of the 1,3,5-triazine ring were not planar, but exhibited a half-chair conformation. The crystal structure was stabilized by a strong intramolecular hydrogen bonding interaction N(3)–H(3)···O(2) and three intermolecular hydrogen bonding interactions, N(2)–H(2)···O(1), N(2)–H(2)···N(4) and N(3)–H(3)···Cl(1). The preliminary bioassay showed that the title compound showed not only aphicidal activity against Sitobion miscanthi (inhibition rate: 74.1%) and Schizaphis graminum (77.5%), but also antifungal activities against Pythium aphanidermatum (62.0%). These results provide valuable guidelines for the design and synthesis of novel aphid control agents and fungicides.
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Tittle, James S., Michael W. Rouse, and Myron L. Braunstein. "Relationship of Static Stereoscopic Depth Perception to Performance with Dynamic Stereoscopic Displays." Proceedings of the Human Factors Society Annual Meeting 32, no. 19 (1988): 1439–42. http://dx.doi.org/10.1177/154193128803201928.
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Although most tasks performed by human observers that require accurate stereoscopic depth perception, such as working with tools, operating machinery, and controlling vehicles, involve dynamically changing disparities, classification of observers as having normal or deficient stereoscopic vision is currently based on performance with static stereoscopic displays. The present study compares the performance of subjects classified as deficient in static stereoscopic vision to a control group with normal stereoscopic vision in two experiments-one in which the disparities were constant during motion and one in which the disparities changed continuously. In the first experiment, subjects judged orientation in depth of a dihedral angle, with the apex pointed toward or away from them. The angle translated horizontally, leaving the disparities constant. When disparity and motion parallax were placed in conflict, subjects in the normal group almost always responded in accordance with disparity, whereas subjects in the deficient group responded in accordance with disparity at chance levels. In the second experiment, subjects were asked to judge the direction of rotation of a computer-generated cylinder. When dynamic occlusion and dynamic disparity indicated conflicting directions, performance of subjects in the normal and deficient groups did not differ significantly. When only dynamic disparity information was provided, most subjects classified as stereo deficient were able to judge the direction of rotation accurately. These results indicate that measures of stereoscopic vision that do not include changing disparities may not provide a complete evaluation of the ability of a human observer to perceive depth on the basis of disparity.
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Ikeda, Susumu, Tsukasa Nakano, Akira Tsuchiyama, et al. "Three-dimensional study by synchrotron radiation computed tomography of melt distribution in samples doped to enhance contrast." Mineralogical Magazine 81, no. 5 (2017): 1203–22. http://dx.doi.org/10.1180/minmag.2016.080.163.
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AbstractThe three-dimensional distribution of melt in partially molten synthetic samples compositionally corresponding to diopside (90 wt.%)–anorthite (10 wt.%) and doped with PbO, WO3, MoO3, or Cs2O to enhance contrast was studied by X-ray computed tomography (CT) with synchrotron radiation. The heavy elements were strongly concentrated in the melt and contributed to an increase of the X-ray linear attenuation coefficient (LAC) of it. PbO was found to be compatible with silicate melt (>20 wt.% in solution) and incompatible with diopside crystals. Other oxides WO3 (∼10 wt.%), MoO3 (∼5 wt.%) and Cs2O (< 5 wt.%) are also soluble only in the melt. Such doping is useful not only for LAC control in X-ray CT measurements, but also for systematic control of the structure (wetting properties, distribution and connectivity) of partial melt. This technique gives basic information for discussion of the 3D distribution of partial melt having different wetting properties. As PbO was most effective in visualization of the diopside–anorthite partially molten system, CT images of the PbO-bearing sample were used for further 3D investigation of distribution. A distribution of dihedral angles at solid-melt-solid triple junctions ranging from 22 to 55° was observed with the 3D data. This range in angle distribution was probably caused by anisotropy of crystals and the result supports the argument that there is some limitation in a theoretical framework of stereology which estimates the 3D structure based on 2D observations. Investigators have begun to apply X-ray CT to the study of the 3D distribution of partial melts in rocks using synchrotron radiation. Our study on the effect of doping is one approach for developing a technique to investigate 3D melt distribution.
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Moriarty, Nigel W., Eli J. Draizen, and Paul D. Adams. "An editor for the generation and customization of geometry restraints." Acta Crystallographica Section D Structural Biology 73, no. 2 (2017): 123–30. http://dx.doi.org/10.1107/s2059798316016570.
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Chemical restraints for use in macromolecular structure refinement are produced by a variety of methods, including a number of programs that use chemical information to generate the required bond, angle, dihedral, chiral and planar restraints. These programs help to automate the process and therefore minimize the errors that could otherwise occur if it were performed manually. Furthermore, restraint-dictionary generation programs can incorporate chemical and other prior knowledge to provide reasonable choices of types and values. However, the use of restraints to define the geometry of a molecule is an approximation introduced with efficiency in mind. The representation of a bond as a parabolic function is a convenience and does not reflect the true variability in even the simplest of molecules. Another complicating factor is the interplay of the molecule with other parts of the macromolecular model. Finally, difficult situations arise from molecules with rare or unusual moieties that may not have their conformational space fully explored. These factors give rise to the need for an interactive editor for WYSIWYG interactions with the restraints and molecule.Restraints Editor, Especially Ligands(REEL) is a graphical user interface for simple and error-free editing along with additional features to provide greater control of the restraint dictionaries in macromolecular refinement.
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Giri, Nitai, and S. Mahapatra. "Optimal control of photodissociation of phenol using genetic algorithm." Journal of Chemical Physics 156, no. 9 (2022): 094305. http://dx.doi.org/10.1063/5.0081282.
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Photodissociation dynamics of the OH bond of phenol is studied with an optimally shaped laser pulse. The theoretical model consists of three electronic states (the ground electronic state, ππ* state, and πσ* state) in two nuclear coordinates (the OH stretching coordinate as a reaction coordinate, r, and the CCOH dihedral angle as a coupling coordinate, θ). The optimal UV laser pulse is designed using the genetic algorithm, which optimizes the total dissociative flux of the wave packet. The latter is calculated in the adiabatic asymptotes of the S0 and S1 electronic states of phenol. The initial state corresponds to the vibrational levels of the electronic ground state and is defined as | n r, n θ⟩, where n r and n θ represent the number of nodes along r and θ, respectively. The optimal UV field excites the system to the optically dark πσ* state predominantly over the optically bright ππ* state with the intensity borrowing effect for the |0, 0⟩ and |0, 1⟩ initial states. For the |0, 0⟩ initial condition, the photodissociation to the S1 asymptotic channel is favored slightly over the S0 asymptotic channel. Addition of one quantum of energy along the coupling coordinate increases the dissociation probability in the S1 channel. This is because the wave packet spreads along the coupling coordinate on the πσ* state and follows the adiabatic path. Hence, the S1 asymptotic channel gets more ([Formula: see text]11%) dissociative flux as compared to the S0 asymptotic channel for the |0, 1⟩ initial condition. The |1, 0⟩ and |1, 1⟩ states are initially excited to both the ππ* and πσ* states in the presence of the optimal UV pulse. For these initial conditions, the S1 channel gets more dissociative flux as compared to the S0 channel. This is because the high energy components of the wave packet readily reach the S1 channel. The central frequency of the optimal UV pulse for the |0, 0⟩ and |0, 1⟩ initial states has a higher value as compared to the |1, 0⟩ and |1, 1⟩ initial states. This is explained with the help of an excitation mechanism of a given initial state in relation to its energy.
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Bobashev, S. V., Yu P. Golovachev, G. A. Kurbatov, et al. "Experimental and numerical investigation into the supersonic flow of a weakly ionized plasma around a dihedral angle: Magnetohydrodynamic control of the flow pattern and heat fluxes toward the wall." Technical Physics 54, no. 1 (2009): 33–41. http://dx.doi.org/10.1134/s1063784209010058.
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Wilga, C. D., and G. V. Lauder. "Three-dimensional kinematics and wake structure of the pectoral fins during locomotion in leopard sharks Triakis semifasciata." Journal of Experimental Biology 203, no. 15 (2000): 2261–78. http://dx.doi.org/10.1242/jeb.203.15.2261.
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The classical theory of locomotion in sharks proposes that shark pectoral fins are oriented to generate lift forces that balance the moment produced by the oscillating heterocercal tail. Accordingly, previous studies of shark locomotion have used fixed-wing aircraft as a model assuming that sharks have similar stability and control mechanisms. However, unlike airplanes, sharks are propelled by undulations of the body and tail and have considerable control of pectoral fin motion. In this paper, we use a new approach to examine the function of the pectoral fins of leopard sharks, Triakis semifasciata, during steady horizontal swimming at speeds of 0.5-2.0ls(−1), where l is total body length, and during vertical maneuvering (rising and sinking) in the water column. The planar orientation of the pectoral fin was measured using three-dimensional kinematics, while fluid flow in the wake of the pectoral fin and forces exerted on the water by the fin were quantified using digital particle image velocimetry (DPIV). Steady horizontal swimming in leopard sharks is characterized by continuous undulations of the body with a positive body tilt to the flow that decreases from a mean of 11 degrees to 0.6 degrees with increasing flow speeds from 0. 5 to 2.0ls(−1). Three-dimensional analysis showed that, during steady horizontal locomotion, the pectoral fins are cambered, concave downwards, at a negative angle of attack that we predict to generate no significant lift. Leopard shark pectoral fins are also oriented at a substantial negative dihedral angle that amplifies roll moments and hence promotes rapid changes in body position. Vortices shed from the trailing edge of the pectoral fin were detected only during vertical maneuvering. Starting vortices are produced when the posterior plane of the pectoral fin is actively flipped upwards or downwards to initiate rising or sinking, respectively, in the water column. The starting vortex produced by the pectoral fin induces a pitching moment that reorients the body relative to the flow. Body and pectoral fin surface angle are altered significantly when leopard sharks change vertical position in the water column. Thus, locomotion in leopard sharks is not analogous to flight in fixed-wing aircraft. Instead, a new force balance for swimming leopard sharks is proposed for steady swimming and maneuvering. Total force balance on the body is adjusted by altering the body angle during steady swimming as well as during vertical maneuvering, while the pectoral fins appear to be critical for initiating maneuvering behaviors, but not for lift production during steady horizontal locomotion.
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Kosk, Robert, Richard Southern, Lihua You, Shaojun Bian, Willem Kokke, and Greg Maguire. "Deep Spectral Meshes: Multi-Frequency Facial Mesh Processing with Graph Neural Networks." Electronics 13, no. 4 (2024): 720. http://dx.doi.org/10.3390/electronics13040720.
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With the rising popularity of virtual worlds, the importance of data-driven parametric models of 3D meshes has grown rapidly. Numerous applications, such as computer vision, procedural generation, and mesh editing, vastly rely on these models. However, current approaches do not allow for independent editing of deformations at different frequency levels. They also do not benefit from representing deformations at different frequencies with dedicated representations, which would better expose their properties and improve the generated meshes’ geometric and perceptual quality. In this work, spectral meshes are introduced as a method to decompose mesh deformations into low-frequency and high-frequency deformations. These features of low- and high-frequency deformations are used for representation learning with graph convolutional networks. A parametric model for 3D facial mesh synthesis is built upon the proposed framework, exposing user parameters that control disentangled high- and low-frequency deformations. Independent control of deformations at different frequencies and generation of plausible synthetic examples are mutually exclusive objectives. A Conditioning Factor is introduced to leverage these objectives. Our model takes further advantage of spectral partitioning by representing different frequency levels with disparate, more suitable representations. Low frequencies are represented with standardised Euclidean coordinates, and high frequencies with a normalised deformation representation (DR). This paper investigates applications of our proposed approach in mesh reconstruction, mesh interpolation, and multi-frequency editing. It is demonstrated that our method improves the overall quality of generated meshes on most datasets when considering both the L1 norm and perceptual Dihedral Angle Mesh Error (DAME) metrics.
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Gorske, Benjamin C., Emily M. Mumford, Charles G. Gerrity, and Imelda Ko. "A Peptoid Square Helix via Synergistic Control of Backbone Dihedral Angles." Journal of the American Chemical Society 139, no. 24 (2017): 8070–73. http://dx.doi.org/10.1021/jacs.7b02319.
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Safina, Brian S., Richard L. Elliott, Andrew K. Forrest та ін. "Design of Selective Benzoxazepin PI3Kδ Inhibitors Through Control of Dihedral Angles". ACS Medicinal Chemistry Letters 8, № 9 (2017): 936–40. http://dx.doi.org/10.1021/acsmedchemlett.7b00170.
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Nalaoh, Phattananawee, Sareeya Bureekaew, Vinich Promarak та Jonathan S. Lindsey. "Fourfold alkyl wrapping of a copper(II) porphyrin thwarts macrocycle π–π stacking in a compact supramolecular package". Acta Crystallographica Section C Structural Chemistry 76, № 7 (2020): 647–54. http://dx.doi.org/10.1107/s2053229620007172.
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Porphyrins are valuable constituents in optoelectronic, catalytic, and other applications, yet control of intermolecular π–π stacking is invariably essential to attain the desired properties. Superstructures built onto the porphyrin, often via meso-aryl groups, can afford facial encumbrance that suppresses π–π stacking, although some molecular designs have provided insufficient facial coverage and many have entailed cumbersome syntheses. In this study, a copper(II) porphyrin bearing four meso substituents, namely, {10,20-bis[2,6-bis(octyloxy)phenyl]-5,15-dibromoporphinato}copper(II), [Cu(C64H82Br2N4O4)], was prepared by metalation of the corresponding free-base porphyrin and was characterized by single-crystal X-ray diffraction. The crystal structure reveals a dihedral angle of 111.1 (2)° for the plane of the meso-aryl group relative to the plane of the porphyrin, with both aryl groups tilted in the same direction. Each of the four octyloxy groups exhibits a gauche conformation for the –OCH2CH2– unit but is extended with four or five anti (–CH2CH2–/H) conformations thereafter, causing each octyl group to span the dimension of the macrocycle. In a global frame of reference where the two Br atoms define the north/south poles and the two aryl groups are at antipodes on the equator, two octyl groups of one aryl unit project over the northern hemisphere (covering pyrroles A and B), whereas those of the other aryl unit project over the southern hemisphere (covering pyrroles C and D). Together, the four octyl groups ensheath the two faces of the porphyrin in a self-wrapped assembly. The closest approach of the Cu atom to an octyl methylene C atom (position 6) is 3.5817 (18) Å, the mean separations of neighboring porphyrin planes are 8.059 (4) and 4.693 (8) Å along the a and c axes, respectively, and the center-to-center distances between the Cu atoms of neighboring porphyrins are 10.2725 (4), 12.2540 (6), and 12.7472 (6) Å along the a, b, and c axes, respectively. The Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots provide information concerning contact interactions in the supramolecular assembly of the solid crystal.
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Nikolaou, Eleftherios, and Vassilis Kostopoulos. "Vee-Tail Preliminary Design Methodology for Class I mini- UAV." Journal of Physics: Conference Series 2716, no. 1 (2024): 012062. http://dx.doi.org/10.1088/1742-6596/2716/1/012062.
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Abstract Unmanned Air Vehicles (UAVs) are becoming increasingly popular and widely used in a variety of industries. They can be used for tasks such as agriculture, construction, delivery, surveillance, rescue operations, mapping, wildlife tracking and many more. With the advancements in technology, UAVs are becoming more autonomous and able to perform tasks with minimal human intervention, so are widely used for military and law enforcement purposes. V-tail configurations are commonly used on UAVs due to their advantages in control and stability performance, as well as their ability to reduce drag and improve overall efficiency. However, research on V-tail design and sizing is limited, particularly for Class I mini-UAVs. The objective of this paper is to identify a methodology for a V-tail sizing of a Class I Mini UAV (NATO classification), which refers to the Conceptual and Preliminary Design of the UAV. The methodology will follow the design of a V-tail from the characteristics of the conventional tail of the UAV. Once the characteristics of the conventional tail were extracted, V-tail geometric characteristics (reference area, aspect ratio, mean aerodynamic chord, tail span, dihedral angle), were computed. Therefore, the aerodynamic characteristics of the V-tail have to be extracted, first as an isolated tail, and then as an installed tail. The stability derivatives of the V-tail are then calculated. The methodology for the analytical aerodynamic characteristics and stability derivatives, is a combination of NACA Report No.823 and Marcello R. Napolitano methodologies. Paul E. Purser and John P. Campbell provide design methods for V-tail on a NACA report, which include some of the desired stability derivatives. The rest of them will be calculated with Napolitano’s method. Marcello R. Napolitano gives a methodology for conventional tail sizing; thus, the equations of its methodology have to convert for a V-tail configuration. Furthermore, the aerodynamic characteristics and stability derivatives of the designed V-tail will be verified by Low Fidelity Aerodynamics simulation (XFLR5 software), and then by High Fidelity Aerodynamics by means of CFD. The results between low fidelity analytical values and High-Fidelity Aerodynamics values indicate a relative error lower than 20%.
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Ceballos Inza, Victor, Panagiotis Fykouras, Florian Rist, et al. "Designing triangle meshes with controlled roughness." ACM Transactions on Graphics 43, no. 6 (2024): 1–20. http://dx.doi.org/10.1145/3687940.
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Motivated by the emergence of rough surfaces in various areas of design, we address the computational design of triangle meshes with controlled roughness. Our focus lies on small levels of roughness. There, roughness or smoothness mainly arises through the local positioning of the mesh edges and faces with respect to the curvature behavior of the reference surface. The analysis of this interaction between curvature and roughness is simplified by a 2D dual diagram and its generation within so-called isotropic geometry, which may be seen as a structure-preserving simplification of Euclidean geometry. Isotropic dihedral angles of the mesh are close to the Euclidean angles and appear as Euclidean edge lengths in the dual diagram, which also serves as a tool for visualization and interactive local design. We present a computational framework that includes appearance-aware remeshing, optimization-based automatic roughening, and control of dihedral angles.
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Feytens, Debby, Grégory Chaume, Gérard Chassaing, et al. "Local Control of the Cis–Trans Isomerization and Backbone Dihedral Angles in Peptides Using Trifluoromethylated Pseudoprolines." Journal of Physical Chemistry B 116, no. 13 (2012): 4069–79. http://dx.doi.org/10.1021/jp300284u.
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Mondal, Nityagopal, Sannyasi Charan Mandal, and Gourab Kanti Das. "Diastereoselectivity in intramolecular ene cyclisation A theoretical study." Canadian Journal of Chemistry 82, no. 4 (2004): 539–50. http://dx.doi.org/10.1139/v04-002.
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Diastereoselectivity in unactivated and activated ene cyclisation can be predicted using HF/6-31G(d) optimized geometry of the transition states. Relative energies of different conformations of the transition states, calculated using DFT, can be used for the prediction of product ratios. It was found that the dihedral angle around the forming carboncarbon bond controls the cistrans diastereoselectivity. A set of three model pericyclic transition structures has been proposed that mimics the activation process of ene cyclisation.Key words: intramolecular ene reaction, ab initio, DFT.
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Edwards, David J., Robin G. Pritchard, and Timothy W. Wallace. "Fine-tuning of biaryl dihedral angles: structural characterization of five homologous three-atom bridged biphenyls by X-ray crystallography." Acta Crystallographica Section B Structural Science 61, no. 3 (2005): 335–45. http://dx.doi.org/10.1107/s0108768105006713.
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The homologous series of three-atom bridged biaryls comprising 5,7-dihydro-1,2,3,9,10,11-hexamethoxydibenzo[c,e]oxepine, 6,7-dihydro-1,2,3,9,10,11-hexamethoxy-6-methyl-5H-dibenzo[c,e]azepinium chloride, 5,7-dihydro-1,2,3,9,10,11-hexamethoxydibenzo[c,e]thiepine, and the 6-oxide and 6,6-dioxide derivatives of the latter have been characterized by X-ray crystal structure analysis. Within this series the endocyclic and exocyclic biaryl dihedral angles vary over 10° ranges, reflecting the changing balance of intramolecular (steric, geometric) and intermolecular (crystal packing) forces, the former being potential control elements for fine-tuning the helicity of the biaryl system.
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Holness, Marian B. "Temperature and pressure dependence of quartz-aqueous fluid dihedral angles: the control of adsorbed H2O on the permeability of quartzites." Earth and Planetary Science Letters 117, no. 3-4 (1993): 363–77. http://dx.doi.org/10.1016/0012-821x(93)90090-v.
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Jeon, Youngeun, Jineun Kim, Gihaeng Kang, and Tae Ho Kim. "Crystal structure of pymetrozine." Acta Crystallographica Section E Crystallographic Communications 71, no. 7 (2015): o461—o462. http://dx.doi.org/10.1107/s2056989015010804.
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The title compound, C10H11N5O {systematic name: 6-methyl-4-[(E)-(pyridin-3-ylmethylidene)amino]-4,5-dihydro-1,2,4-triazin-3(2H)-one}, C10H11N5O, is used as an antifeedant in pest control. The asymmetric unit comprises two independent molecules,AandB, in which the dihedral angles between the pyridinyl and triazinyl ring planes [r.m.s. deviations = 0.0132 and 0.0255 ] are 11.60 (6) and 18.06 (4)°, respectively. In the crystal, N—H...O, N—H...N, C—H...N and C—H...O hydrogen bonds, together with weak π–π interactions [ring-centroid separations = 3.5456 (9) and 3.9142 (9) Å], link the pyridinyl and triazinyl rings ofAmolecules, generating a three-dimensional network.
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Al-Khaykanee, Mohsin, та Ali Al-Jawdahb. "Effect of π-conjugated molecules on electronics properties of benzene-diamine derivatives". Iraqi Journal of Physics (IJP) 19, № 50 (2021): 70–76. http://dx.doi.org/10.30723/ijp.v19i50.658.
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The present work shows a theoretical results that have been used the functional Hybrid of three parameters Lee-Yang-Parr (B3LYP) of the quantum mechanical approach for density functional theory with (Spanish Initiative for Electronic Simulations with Thousands of Atoms) SIESTA code. All calculations were carried out employing the used method at the Gaussian 09 package of programs. It was reported the main point for research on dominance of the bandgap of elongated pi-conjugated molecules by using different chemical groups replacing hydrogen atom in the most molecules that used in this work. The side groups creates another factor that controls the value of the band gap. The dihedral angle between the two phenyl rings plays more important role in controlling the band gap in these molecules.
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Romanova, Viktoryna A. "Visualizing surface formation of semi-regular polyhedra of Archimedes." Structural Mechanics of Engineering Constructions and Buildings 16, no. 4 (2020): 279–89. http://dx.doi.org/10.22363/1815-5235-2020-16-4-279-289.
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The most common method of forming semi-control polyhedra consists in cutting off angles and ribs of regular polyhedra by planes. The aim of the work - to consider the automated formation of a number of surfaces of semi-regular Archimedean polyhedra based on the dodecahedron. These include the truncated dodecahedron, the icosododecahedron, the romboicosododecahedron and the truncated icosododecahedron. The formation of surfaces is carried out by the kinematic method in AutoCAD using programs compiled in the AutoLISP language. Methods. The methodology for the formation of these polyhedra provides for truncation of the angles and edges of the dodecahedron. This requires the calculation of a number of geometric parameters of these polyhedra and dodecahedron, such as the value of the truncation of the dodecahedron edges, the size of the edges of truncated polyhedra, the centers of faces, dihedral angles, etc. In order to generate these surfaces, a frame is constructed because the frame lines are used as guides to form surfaces in a kinematic way. The electronic model of each polyhedron is constructed as a set of compartments of surfaces of all its faces, and each compartment is assigned to a certain layer of the drawing. The frame and electronic model of the polyhedra under study are formed by means of user programs composed in the functional language AutoLISP. The process of forming surfaces of selected polyhedra in the AutoCAD environment is provided by special programs that are also compiled in the AutoLISP language. Results. Software was created to demonstrate the process of formation of a number of Archimedes polyhedra on the monitor screen.
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Hong, Tzung-Pei, Ming-Jhe Hu, Tang-Kai Yin, and Shyue-Liang Wang. "A Multi-Scale Convolutional Neural Network for Rotation-Invariant Recognition." Electronics 11, no. 4 (2022): 661. http://dx.doi.org/10.3390/electronics11040661.
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The Internet of things (IoT) enables mobile devices to connect and exchange information with others over the Internet with a lot of applications in consumer, commercial, and industrial products. With the rapid development of machine learning, IoT with image recognition capability is a new research area to assist mobile devices with processing image information. In this research, we propose the rotation-invariant multi-scale convolutional neural network (RIMS-CNN) to recognize rotated objects, which are commonly seen in real situations. Based on the dihedral group D4 transformations, the RIMS-CNN equips a CNN with multiple rotated tensors and its processing network. Furthermore, multi-scale features and shared weights are employed in the RIMS-CNN to increase performance. Compared with the data augmentation approach of using rotated images at random angles for training, our proposed method can learn inherent convolution kernels for rotational features. Experiments were conducted on the benchmark datasets: MNIST, FASHION-MNIST, CIFAR-10, and CIFAR-100. Significant improvements over the other models were achieved to show that rotational invariance could be learned.
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Ren, Yi, Semin Lee, Jeffery Bertke, Danielle L. Gray, and Jeffrey S. Moore. "Synthesis and structures of 11,11,12,12-tetracyano-2,6-diiodo-9,10-anthraquinodimethane and its 2:1 cocrystals with anthracene, pyrene and tetrathiafulvalene." Acta Crystallographica Section C Structural Chemistry 72, no. 12 (2016): 923–31. http://dx.doi.org/10.1107/s2053229616016387.
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Radical salts and charge-transfer complexes (CTCs) containing tetracyanoquinodimethane (TCNQ) display electrical conductivity, which has led to the development of many TCNQ derivatives with enhanced electron-accepting properties that are applicable toward organic electronics. To expand the family of TCNQ derivatives, we report the synthesis and structures of 11,11,12,12-tetracyano-2,6-diiodo-9,10-anthraquinodimethane (abbreviated as DITCAQ), C20H6I2N4, and its charge-transfer complexes with various electron donors, namely DITCAQ–anthracene (2/1), C20H6I2N4·0.5C14H10, (I), DITCAQ–pyrene (2/1), C20H6I2N4·0.5C16H10, (II), and DITCAQ–tetrathiafulvalene (2/1), C20H6I2N4·0.5C6H4S4, (III). The molecular structure of DITCAQ consists of a 2,6-diiodo-9,10-dihydroanthracene moiety with two malononitrile substituents. DITCAQ possesses a saddle shape, since the malononitrile groups bend significantly up out of the plane of the central ring and the two benzene rings bend down out of the same plane. π–π interactions between DITCAQ and the electron-donor molecules control the degree of charge transfer in cocrystals (I), (II), and (III), which is reflected in both the dihedral angles between the terminal benzene ring and the central ring on the DITCAQ motifs, and their corresponding IR spectra.
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Ysasi, Alexandra B., Willi L. Wagner, Robert D. Bennett, et al. "Remodeling of alveolar septa after murine pneumonectomy." American Journal of Physiology-Lung Cellular and Molecular Physiology 308, no. 12 (2015): L1237—L1244. http://dx.doi.org/10.1152/ajplung.00042.2015.
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In most mammals, removing one lung (pneumonectomy) results in the compensatory growth of the remaining lung. In mice, stereological observations have demonstrated an increase in the number of mature alveoli; however, anatomic evidence of the early phases of alveolar growth has remained elusive. To identify changes in the lung microstructure associated with neoalveolarization, we used tissue histology, electron microscopy, and synchrotron imaging to examine the configuration of the alveolar duct after murine pneumonectomy. Systematic histological examination of the cardiac lobe demonstrated no change in the relative frequency of dihedral angle components (Ends, Bends, and Junctions) ( P > 0.05), but a significant decrease in the length of a subset of septal ends (“E”). Septal retraction, observed in 20–30% of the alveolar ducts, was maximal on day 3 after pneumonectomy ( P < 0.01) and returned to baseline levels within 3 wk. Consistent with septal retraction, the postpneumonectomy alveolar duct diameter ratio (Dout:Din) was significantly lower 3 days after pneumonectomy compared to all controls except for the detergent-treated lung ( P < 0.001). To identify clumped capillaries predicted by septal retraction, vascular casting, analyzed by both scanning electron microscopy and synchrotron imaging, demonstrated matted capillaries that were most prominent 3 days after pneumonectomy. Numerical simulations suggested that septal retraction could reflect increased surface tension within the alveolar duct, resulting in a new equilibrium at a higher total energy and lower surface area. The spatial and temporal association of these microstructural changes with postpneumonectomy lung growth suggests that these changes represent an early phase of alveolar duct remodeling.
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Rushmer, Tracy. "Melt segregation in the lower crust: how have experiments helped us?" Earth and Environmental Science Transactions of the Royal Society of Edinburgh 87, no. 1-2 (1996): 73–83. http://dx.doi.org/10.1017/s0263593300006490.
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ABSTRACT:The rheological and chemical behaviour of the lower crust during anatexis has been a major focus of geological investigations for many years. Modern studies of crustal evolution require significant knowledge, not only of the potential source regions for granites, but also of the transport paths and emplacement mechanisms operating during granite genesis. We have gained significant insights into the segregation and transport of granitoid melts from the results of experimental studies on rock behaviour during partial melting. Experiments performed on crustal rock cores under both hydrostatic conditions and during deformation have led, in part, to two conclusions. (1) The interfacial energy controlling melt distribution is anisotropic and, as a result, the textures deviate significantly from those predicted for ideal systems—planar solid-melt interfaces are developed in addition to triple junction melt pockets. The ideal dihedral angle model for melt distribution cannot be used as a constraint to predict melt migration in the lower crust. (2) The ‘critical melt fraction’ model, which requires viscous, granitic melt to remain in the source until melt fractions reach >25 vol%, is not a reliable model for melt segregation. The most recent experimental results on crustal rock cores which have helped advance our understanding of melt segregation processes have shown that melt segregation is controlled by several variables, including the depth of melting, the type of reaction and the volume change associated with that reaction. Larger scale processes such as tectonic environment determine the rate at which the lower crust heats and deforms, thus the tectonic setting controls the melt fraction at which segregation takes place, in addition to the pressure and temperature of the potential melting reactions. Melt migration therefore can occur at a variety of different melt fractions depending on the tectonic environment; these results have significant implications for the predicted geochemistry of the magmas themselves.
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Li, Wanqing, Marcos D. Battistel, Hannah Reeves, et al. "A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic." Glycobiology 30, no. 10 (2020): 787–801. http://dx.doi.org/10.1093/glycob/cwaa040.
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Abstract O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at −10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.
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Huang, Xiaoqiang, Robin Pearce, and Yang Zhang. "FASPR: an open-source tool for fast and accurate protein side-chain packing." Bioinformatics 36, no. 12 (2020): 3758–65. http://dx.doi.org/10.1093/bioinformatics/btaa234.
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Abstract Motivation Protein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory. Results We present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20°, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3 s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies. Availability and implementation The web server, source code and datasets are freely available at https://zhanglab.ccmb.med.umich.edu/FASPR and https://github.com/tommyhuangthu/FASPR. Supplementary information Supplementary data are available at Bioinformatics online.
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Ogurtani, Tarik Omer. "Irreversible thermodynamics of surfaces and interfaces: Special reference to the strained thin solid films on the substrates: Theory and practice." Journal of Applied Physics 133, no. 15 (2023): 155301. http://dx.doi.org/10.1063/5.0138741.
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The realization of nanoscale devices largely depends on our ability to control and manipulate interfacial interactions and, thus, understanding of the mechanisms of surface/interface instabilities. In this work, theoretically as well as technologically important and distinct two thermodynamic systems, which are exposed to (isobaric) and isolated from (isochoric) external body forces and surface tractions, are formulated by using irreversible thermodynamics in combination with the generalized variational method. The starting point for the present formulation closely follows up the Fowler and Guggenheim [ Statistical Thermodynamics (University Press, Cambridge, 1952)] interpretation of the Planck inequality [Über Prinzip Vermehrung Entropie: Ann. Phys. Series 2(32), 462 (1887)] for isothermal reversible and irreversible (natural) infinitesimal changes in heterogeneous systems (multi-phase and multi-component). By combining this fundamental principle with the interlink between the dissipation function and global internal entropy production postulates, two distinct sets of governing equations for the surface drift-diffusion flux as well as the rate of evaporation/condensation and/or the growth/recrystallization of amorphous solid thin films are obtained for isochoric and isobaric systems. The role of Eshelby's energy-momentum tensor in the generalized potential for the interface displacement is found to differ (opposite in sign) for isochoric and isobaric systems. To demonstrate the importance of these sign conflicts, two sets of computer experiments are performed on isochoric and isobaric systems. They showed us that the elastic strain energy density contribution to the generalized driving force for surface drift-diffusion alone favoring flat and smooth surfaces in isobaric systems regardless of the sign of the uniaxial stress (healing), rather than causing the surface roughness and even catastrophic crack initiation as the case in internally strained isochoric systems. Computer simulations allowed us to track down the dynamical behavior of test modules by furnishing surface and strain energy variations, combined with the Global Helmholtz free change, which indicates the existence of two regimes: initial smooth surface undulations followed up by the rather chaotic crack formation and propagation stage at the middle of the thin film supported by the stiff substrate. In this study, we mainly focused on the development kinetics of “Stranski–Krastanow” island-type morphology, initiated by the nucleation route rather than the surface roughening scheme. The physicomathematical model, which is based on the irreversible thermodynamics treatment of surfaces and interfaces with singularities [T. O. Ogurtani, J. Chem. Phys. 124, 144706 (2006)], furnishes us to have autocontrol on otherwise free-motion of the triple junction contour line between the substrate and the droplet without presuming any equilibrium dihedral contact (wetting) angles at edges. We have also demonstrated the formation of the Stranski–Krastanow (SK)-type doublet islanding (quantum dots) as a stationary nonequilibrium state in an epitaxially strained thin flat droplet on a rigid substrate by introducing the wetting potential—invoked by the quantum confinement—into the scenario and carefully selecting the system parameters (size and shape) for the isochoric system represented by [Ge/Si (100)]. It has been also shown that on the contrary to common perceptions, the Stranski–Krastanow islands are in genuine stationary nonequilibrium states in the sense of Prigogine if one invokes proper free-moving boundary conditions at triple junctions deduced from the irreversible thermodynamics rather than ad hoc periodic or reflecting constrains at the edges.
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López Peña, Hugo A., Jacob M. Shusterman, Derrick Ampadu Boateng, Ka Un Lao, and Katharine Moore Tibbetts. "Coherent Control of Molecular Dissociation by Selective Excitation of Nuclear Wave Packets." Frontiers in Chemistry 10 (April 5, 2022). http://dx.doi.org/10.3389/fchem.2022.859095.
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We report on pump-probe control schemes to manipulate fragmentation product yields in p-nitrotoluene (PNT) cation. Strong field ionization of PNT prepares the parent cation in the ground electronic state, with coherent vibrational excitation along two normal modes: the C–C–N–O torsional mode at 80 cm−1 and the in-plane ring-stretching mode at 650 cm−1. Both vibrational wave packets are observed as oscillations in parent and fragment ion yields in the mass spectrum upon optical excitation. Excitation with 650 nm selectively fragments the PNT cation into C7H7+, whereas excitation with 400 nm selectively produces C5H5+ and C3H3+. In both cases the ion yield oscillations result from torsional wave packet excitation, but 650 and 400 nm excitation produce oscillations with opposite phases. Ab initio calculations of the ground and excited electronic potential energy surfaces of PNT cation along the C–C–N–O dihedral angle reveal that 400 nm excitation accesses an allowed transition from D0 to D6 at 0° dihedral angle, whereas 650 nm excitation accesses a strongly allowed transition from D0 to D4 at a dihedral angle of 90°. This ability to access different electronic excited states at different locations along the potential energy surface accounts for the selective fragmentation observed with different probe wavelengths. The ring-stretching mode, only observed using 800 nm excitation, is attributed to a D0 to D2 transition at a geometry with 90° dihedral angle and elongated C–N bond length. Collectively, these results demonstrate that strong field ionization induces multimode coherent excitation and that the vibrational wave packets can be excited with specific photon energies at different points on their potential energy surfaces to induce selective fragmentation.
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Oktay, Tugrul, and Yüksel Eraslan. "Autonomous flight performance optimization of fixed-wing unmanned aerial vehicle with morphing wingtip." Aircraft Engineering and Aerospace Technology, March 29, 2024. http://dx.doi.org/10.1108/aeat-09-2022-0262.
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Purpose The purpose of this paper is to improve autonomous flight performance of a fixed-wing unmanned aerial vehicle (UAV) via simultaneous morphing wingtip and control system design conducted with optimization, computational fluid dynamics (CFD) and machine learning approaches. Design/methodology/approach The main wing of the UAV is redesigned with morphing wingtips capable of dihedral angle alteration by means of folding. Aircraft dynamic model is derived as equations depending only on wingtip dihedral angle via Nonlinear Least Squares regression machine learning algorithm. Data for the regression analyses are obtained by numerical (i.e. CFD) and analytical approaches. Simultaneous perturbation stochastic approximation (SPSA) is incorporated into the design process to determine the optimal wingtip dihedral angle and proportional-integral-derivative (PID) coefficients of the control system that maximizes autonomous flight performance. The performance is defined in terms of trajectory tracking quality parameters of rise time, settling time and overshoot. Obtained optimal design parameters are applied in flight simulations to test both longitudinal and lateral reference trajectory tracking. Findings Longitudinal and lateral autonomous flight performances of the UAV are improved by redesigning the main wing with morphing wingtips and simultaneous estimation of PID coefficients and wingtip dihedral angle with SPSA optimization. Originality/value This paper originally discusses the simultaneous design of innovative morphing wingtip and UAV flight control system for autonomous flight performance improvement. The proposed simultaneous design idea is conducted with the SPSA optimization and a machine learning algorithm as a novel approach.
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Oh, Chan Seok, Sa Pereira Daniel de, Si Hyun Han, et al. "Dihedral Angle Control of Blue Thermally-Activated Delayed Fluorescent Emitters through Donor Substitution Position for Efficient Reverse Intersystem Crossing." September 21, 2018. https://doi.org/10.5281/zenodo.3556191.
Full textAbstract:
This study shows a molecular design strategy for controlling the dihedral angle of two carbazole donors linked to a 2,4-diphenyl-1,3,5-triazine acceptor by a phenyl unit. Using this approach, six thermally-activated delayed fluorescence emitters were synthesised with donors placed in various positions around a central phenyl core and the photophysical relationship between the donor position and its dihedral angle was investigated. We demonstrate that this angle can affect both the strength of the charge transfer state and the conjugation across the entire molecule, effectively changing the singlet-triplet energy gap of the system. We conclude that materials containing two substituted -<em>ortho</em> donors or one -<em>ortho</em> and an adjacent -<em>meta</em> have the smallest energy gaps and the shortest delayed fluorescence lifetimes. On the other hand, emitters with no -<em>ortho</em> substituted donors have larger energy gaps and slow-to-negligible delayed fluorescence. When applying these materials to organic light-emitting diodes , these blue-emitting devices have a range of electrical properties, the best producing efficiencies as high as 21.8% together with high resistance to roll-off that correlate with the rISC rates obtained.