Relevant bibliographies by topics / Dihedral angles

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Academic literature on the topic 'Dihedral angles'

Author: Grafiati
Published: 4 June 2021
Last updated: 4 February 2022

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Journal articles on the topic "Dihedral angles"

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Horálek, Vratislav. "Stereology of dihedral angles." Applications of Mathematics 45, no. 6 (December 2000): 411–17. http://dx.doi.org/10.1023/a:1022329432636.

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Priestle, John P. "Improved dihedral-angle restraints for protein structure refinement." Journal of Applied Crystallography 36, no. 1 (January 21, 2003): 34–42. http://dx.doi.org/10.1107/s0021889802018265.

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Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages,X-PLOR, and its successor,CNS. Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.
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Gubernat, Agnieszka, and Ludosław Stobierski. "Dihedral angles in silicon carbide." Ceramics International 29, no. 8 (January 2003): 961–65. http://dx.doi.org/10.1016/s0272-8842(03)00053-1.

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Atavin, E. G., and L. V. Vilkov. "Dihedral Angles in Cyclic Molecules." Journal of Structural Chemistry 44, no. 5 (September 2003): 846–51. http://dx.doi.org/10.1023/b:jory.0000029823.17159.0b.

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Oldmixon, E. H., J. P. Butler, and F. G. Hoppin. "Dihedral angles between alveolar septa." Journal of Applied Physiology 64, no. 1 (January 1, 1988): 299–307. http://dx.doi.org/10.1152/jappl.1988.64.1.299.

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To determine the dihedral angle, alpha, at the characteristic three-way septal junctions of lung parenchyma, we examined photomicrographs of sections. The three angles, A, formed where three septal traces meet on section, were measured and found to range between approximately 50 and 170 degrees. Theoretical considerations predicted that the dispersion of alpha is much narrower than that of A. The mean of A and alpha is identically 120 degrees. The standard deviation of alpha was inferred from the cumulative distribution function of A. In lungs inflated to 30 cmH2O (VL30), the standard deviation of alpha was very small (approximately 2 degrees) and increased to approximately 6 degrees in lungs inflated to 0.4 VL30. These findings imply that at VL30 tensions exerted by septa are locally homogeneous (2% variation) and at lower lung volumes become less so (6% variation). At high distending pressures, tissue forces are thought to dominate interfacial forces, and therefore the local uniformity of tensions suggests a stress-responsive mechanism for forming or remodeling the connective tissues. The source of the local nonuniformity at lower volumes is unclear but could relate to differences in mechanical properties of alveolar duct and alveoli. Finally, local uniformity does not imply global uniformity.
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Sugimoto, Nobuo, and Atsushi Minato. "Retroreflector with acute dihedral angles." Optics Letters 19, no. 20 (October 15, 1994): 1660. http://dx.doi.org/10.1364/ol.19.001660.

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Cho, Eung Chun. "Dihedral angles of n-simplices." Applied Mathematics Letters 5, no. 4 (July 1992): 55–57. http://dx.doi.org/10.1016/0893-9659(92)90087-p.

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-M. Schlenker, J. "Dihedral Angles of Convex Polyhedra." Discrete & Computational Geometry 23, no. 3 (March 2000): 409–17. http://dx.doi.org/10.1007/pl00009509.

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Hogervorst, M. A., and R. A. Eagle. "Accurate Recovery of Structure from Motion under Perspective Projection." Perception 26, no. 1_suppl (August 1997): 176. http://dx.doi.org/10.1068/v970375.

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For small objects rotating over a small angle, the 3-D structure and motion are inseparable. Increasing the angle of rotation helps to define image accelerations while increasing the angular size of the object produces greater perspective effects. Both of these cues could be used by the visual system to disambiguate the structure and motion. In a 2 × 2 design we tested the influence of angular size (8 deg ‘S’ or 32 deg ‘L’) and projection type (perspective ‘P’ or orthographic ‘O’) on the perceived dihedral angle of vertically hinged planes (‘open books’). Stimuli depicted hinged planes with dihedral angles ranging from 35° to 169° rotating over angles ranging from 2° to 58°. The task of the subjects was to match the perceived dihedral angle to that of a probe defined by motion, texture, and binocular disparities. Spearman rank order correlations of subjects' settings with the simulated dihedral angles were high in condition LP ( r=0.93) and decreased in the order LP>=SP>=SO>=LO. In the same order, correlations with the total displacement of the projected points increased, up to r=−0.94 in condition LO, indicating that structure and motion become more and more confounded. While for small rotations and small dihedral angles, the settings are heavily influenced by the amount of rotation, for larger rotations and larger dihedral angles settings are more constant over rotation. These results show that both image acceleration and perspective effects play an important role in increasing the veridicality of perceived structure from motion.
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Bakare, Oladapo, Candice Thompson, Yakini Brandy, and Ray J. Butcher. "2-Chloro-N-(2-chlorobenzoyl)-N-(2-ethyl-4-oxo-3,4-dihydroquinazolin-3-yl)benzamide." Acta Crystallographica Section E Structure Reports Online 70, no. 4 (March 29, 2014): o503—o504. http://dx.doi.org/10.1107/s1600536814006035.

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In the title compound, C24H17Cl2N3O3, the quinazolinone ring system is close to planar (r.m.s. deviation = 0.0132 Å), with the imide unit almost perpendicular to it, subtending a dihedral angle of 89.1 (1)°. However, the imide unit itself is not planar, the dihedral angle between the two O=C—N components being 34.6 (1)°. The dihedral angle between the two chlorobenzene rings is 40.50 (7)°, while the angles between these rings and the imide moiety are 54.6 (1) and 58.2 (1)°, respectively. The dihedral angles between the 2-chlorophenyl rings and the quinazolinone ring system are 48.77 (5) and 32.92 (7)° for ringsAandB, respectively. In the crystal, weak C—H...O interactions link the molecules into a three-dimensional array.
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Dissertations / Theses on the topic "Dihedral angles"

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Almeida, Camila de. "An?lise da deforma??o p?s-Rifte na Bacia do Araripe, Nordeste do Brasil." Universidade Federal do Rio Grande do Norte, 2010. http://repositorio.ufrn.br:8080/jspui/handle/123456789/18802.

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Made available in DSpace on 2015-03-13T17:08:28Z (GMT). No. of bitstreams: 1 CamilaA_DISSERT_1-52.pdf: 4763596 bytes, checksum: 04aa5b36a81ca3019e267dac640c6e31 (MD5) Previous issue date: 2010-02-25
The Araripe Basin is located over Precambrian terrains of the Borborema Province, being part of Northeast Brazil inner basins. Its origin is related to the fragmentation of the Gondwana supercontinent and consequently opening of South Atlantic during early Cretaceous. The basin has a sedimentary infill encompassing four distinct evolution stages, comprising Paleozoic syneclisis, pre-rift, rift and post-rift. The target of this study comprises the post-rift section of the basin focusing deformational styles which affect evaporates from Ipubi Member of the Santana Formation, which is composed by gypsum and anidrite layers interbedded with shales. These units occur widespread across the basin. In the central part of the basin, near Nova Olinda-Santana do Cariri, evaporites are affected by an essentialy brittle deformation tipified by fibrous gypsum filled fractures, cutting massive layers of gypsum and anidrite. Veins with variable orientations and dips are observed in the region distributed over three main populations: i) a dominant NWSE with shallow to moderate NE dipping population, consisting of gypsum filled veins in which fibers are normal to vein walls; i) NE-SW veins with moderate SE dips containing subhorizontal growth fibers; and iii) N-S veins with shallow E-W dips with fibers oblique to vein walls. In the west portion of the basin, near Trindade-Ipubi-Araripina towns, evaporate layers are dominantly constituted by gypsum/anidrite finely stratified, showing a minor density of veins. These layers are affected by a unique style of deformation, more ductile, typified by gentle to open horizontal normal folding with several tens of meters length and with double plunging NW-SE or NE-SW hinges, configuring domic features. In detail, gypsum/anidrite laminae are affected by metre to decimeter scale close to tight folding, usually kinked, with broken hinges, locally turning into box folds. Veins show NE-SW main directions with shallow NE dips, growth fibers are parallel to vein walls, constituting slickenfibers. This region is marked by faults that affect Araripina Formation with NW-SE, NE-SW and E-W directions. The main structural styles and general orientations of structures which affected the post-rift section of Araripe Basin yielded important kinematic information analysis which led us to infer a E-W to NE-SW extension direction to the northeastern part of the Basin, whereas in the southeastern part, extension occurred in N-S direction. Thus, it was possible to determine a regional kinematic setting, through this analysis, characterizing a NE-SW to ENE-WSW system for the post-rift section, which is compatible with the tension settings for the Sout American Plate since Albian. Local variations at the fluid pressure linked (or not) to sedimentary overload variation define local tension settings. This way, at the northeastern portion of the basin, the post-rift deformation was governed by a setting which ? 1 is sub-horizontal trending NE-SW and, ? 3 is sub-vertical, emphasizing a reverse fault situation. At the southwestern portion however there was characterized a strike slip fault setting, featuring ? 1 trending ENEWSW and ?3 trending NNW-SSE
A Bacia do Araripe est? inserida sobre os terrenos pr?-cambrianos da Prov?ncia Borborema, fazendo parte das bacias interiores do Nordeste do Brasil. Sua origem est? relacionada ? fragmenta??o do supercontinente Gondwana e consequente abertura do Atl?ntico Sul durante o Cret?ceo Inferior. Possuindo um preenchimento sedimentar que abrange quatro est?gios distintos de sua evolu??o, compreendendo as tectonossequ?ncias de Sin?clise Paleoz?ica, Pr?- Rifte, Rifte e P?s-Rifte. O objeto de estudo deste trabalho, compreende a se??o p?srifte da bacia, focando os estilos deformacionais que afetam os evaporitos do Membro Ipubi da Forma??o Santana, constitu?da por camadas de gipsita e anidrita intercaladas com folhelho, de ocorr?ncia abrangente em toda a Bacia do Araripe Na parte Norte da bacia, nas proximidades de Nova Olinda-Santana do Cariri os evaporitos s?o afetados por uma deforma??o essencialmente fr?gil, tipificada por fraturas preenchidas por gipsita fibrosa, recortando camadas de gipsita e anidrita geralmente maci?as. Na regi?o s?o observados veios com orienta??es e mergulhos bastante variados, distribuindo-se segundo tr?s popula??es principais: (i) uma com dire??o dominante NW-SE, com mergulhos suaves a moderados essencialmente para NE, geralmente preenchidos por gipsita cujas fibras disp?em-se ortogonalmente ?s paredes dos veios; (ii) veios NE-SW com mergulhos moderados para SE, contendo fibras de crescimento suborizontais; e (iii) veios N-S, com mergulhos suaves para E-W, cujas as fibras encontram-se obliquas ?s paredes desses veios. Na regi?o oeste da bacia, nas proximidades de Trindade-Ipubi-Araripina a camadas de evaporitos s?o dominantemente constitu?das por gipsita/anidrita finamente estratificada, apresentando uma densidade menor de veios. Essas camadas s?o afetadas por uma deforma??o peculiar, de car?ter mais d?ctil , tipificada por dobras horizontais, de perfil suave a aberto, com comprimento de onda de v?rias dezenas de metros, n?o raro apresentando charneiras com duplo caimento, com orienta??es NWSE ou NE-SW, constituindo fei??es d?micas. Em detalhe, as l?minas de gipsita/anidrita tamb?m s?o afetadas por dobras de escala m?trica a decim?trica, em geral de perfil fechado a apertado, muitas vezes apresentando estilo em kink (n?o ? raro nestes casos ocorrer ruptura da charneira), localmente constituindo dobras em caixa. Os veios (ocorrendo de forma mais rara) apresentam dire??es principais NE-SW, com mergulhos suaves para SE, as fibras de crescimento disp?em-se paralelamente ?s paredes dos veios, funcionando como slickenfibers. Est? regi?o ? marcada pelas falhas que afetam as rochas da Forma??o Araripina apresentando dire??es NW-SE, NE-SW e E-W. De posse das an?lises dos estilos e da orienta??o geral das estruturas que afetam a se??o p?s-rifte na Bacia do Araripe, atrav?s do m?todo dos diedros retos, foram obtidas informa??o importante quanto ? an?lise cinem?tica da deforma??o, possibilitando assim, definir os sentidos de transporte tect?nico predominantes e a infer?ncia do estado de paleotens?es que governou a instala??o das estruturas tect?nicas presentes. Sendo assim, foi poss?vel definir um regime cinem?tico regional, a partir desta an?lise, caracterizado a se??o p?s-rifte por um sistema de compress?o NE-SW a ENEWSW, regime este condizente com o que vem atuando na Placa Sul-Americana desde, pelo menos, o Albiano. Varia??es locais da press?o de fluidos somadas (ou n?o) a varia??es da sobrecarga sedimentar definem regimes cinem?ticos particulares. Assim, na por??o nordeste da bacia, a deforma??o p?s-rifte foi governada por um regime em que ?1 ? suborizontal e apresenta dire??o NE-SW, e ?3 ? subvertical, denotando um regime de falha inversa . J? na por??o sudoeste da Bacia do Araripe foi caracterizado um regime de falha transcorrente , apresentando ?1 na dire??o ENE-WSW e ?3 orientado segundo NNW-SSE
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Cote, Yoann. "Theory and molecular dynamics simulations of the local dynamics and free energy profiles of proteins : application to the interpretation of protein NMR data." Thesis, Dijon, 2012. http://www.theses.fr/2012DIJOS075.

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Comprendre la dynamique locale des protéines dans leur état natif (structure repliée etfonctionnelle) est essentiel pour comprendre leur dynamique globale et leur fonction biologique. Aucours de cette thèse, nous avons étudié la dynamique locale de plusieurs petites protéines enmesurant les fluctuations de sondes locales le long de la séquence d’acide aminé de ces protéines.Nous avons essayé de comprendre la dynamique de ces sondes locales, comment celles-ci serelaxaient entre leurs différentes conformations, comment leurs fluctuations étaient corrélées lesunes aux autres et comment peuvent-elles être reliées à la fonction biologique des protéines.Dans les trois premiers chapitres, nous introduisons les concepts du mouvement Browniende rotation libre, de la spectroscopie par Résonance Magnétique Nucléaire (RMN) et de ladynamique moléculaire (DM). Dans les chapitres 4 et 5, nous avons étudié la dynamique desliaisons amides de la chaine principale (backbone) des protéines sur leurs paysages d’énergie libre.Dans le chapitre 4, nous avons démontré que les fluctuations des liaisons amide dubackbone de la protéine VA3 sont décrites par une diffusion rotationnelle anormale plutôt que parune diffusion rotationnelle libre généralement utilisée pour interpréter les données RMN enrelaxation de spins et en couplage résiduel dipolaire. [...] Dans le chapitre 5, nous avons démontré la diffusion rotationnelle anormale de ces liaisons jusqu’à une échelle de temps de 100 ns en utilisant dix simulations de DM de 1 μs de la protéineUbiquitine. Nous avons aussi étudié la convergence des paramètres RMN extraits des trajectoiresde DM en fonction de leur durée. [...] Dans le chapitre 6, nous avons réalisé une l’étude de la corrélation entre les mouvements du backbone et des chaines latérales des protéines. [...] Dans la première partie du dernier chapitre de cette thèse, nous avons étudié l’évolution de la corrélation dynamique entre les chaines latérales et la chaine principale d’une protéine durant des évènements de dépliement/repliement. Pour cette étude préliminaire, nous avons utilisé unesimulation de DM d’un « ultra-fast folder » nommé Trp-cage réalisée à 380K. Nous avons confirméles résultats précédemment trouvés pour les protéines dans leur état natif. Nous avons observél’augmentation de la corrélation entre les séries temporelles yn(t) and δn(t) pendant un évènementde dépliement caractérisé par la sortie du tryptophane de sa cage. Un paramètre stérique s aégalement été défini afin de quantifier les intéractions des chaines latérales avec leurenvironnement. Dans une seconde partie de ce dernier chapitre, nous présentons une étudepréliminaire du dépliement d’un « downhill folder » nommé gpW sous contrainte d’une force. Pourcaractériser le dépliement de la protéine gpW, nous avons calculé les chemical shifts des atomes Cª et Hⁿ du backbone le long de sa séquence en fonction d’une coordonnée réactionnelle choisie comme étant la distance entre les Cª de résidus C- et N- terminaux. Nous avons démontré qu’il était difficile de discerner un comportement particulier à partir des tous les chemical shifts en fonction de la distance. Cependant, en moyennant la valeur des chemical shifts en sur tous lesrésidus de la protéine nous trouvons que l’évolution de cette valeur moyenne en fonction de ladistance permettait de décrire les évènements du dépliement de la protéine en fonction de lacoordonnée de réaction durant la simulation de DM
Understand the local dynamics of proteins in their native state, i.e. in their folded functionalstructure, is a prerequisite to understand their global dynamics and their biological function. In thepresent thesis, we investigated the local dynamics of several small proteins by recording thefluctuations of local probes along the amino-acid sequence of those proteins. We tried tounderstand the dynamics of the local probe, i.e. how they relax between their differentconformations, how their fluctuations are correlated to each other, how their fluctuations arerelated to the function of the proteins. In the first three chapters, we introduced the concepts of the free rotational Brownian motion, of the Nuclear Magnetic Resonance spectroscopy and of the Molecular Dynamics (MD)simulations. In chapters 4 and 5, we studied the dynamics of the backbone amide bonds of theproteins on their free-energy landscape. In chapter 4, we demonstrated that the fluctuations of the backbone amide bonds of the protein VA3 are described by a rotational anomalous diffusion rather than by a free rotationaldiffusion, as often assumed in the interpretation of the raw NMR-measured data (Spin relaxation(SR) data and Residual Dipolar Coupling (RDC) data. [...] In chapter 5, we demonstrated the anomalous diffusion of backbone amide bonds up to 100 ns by using ten MD trajectories of 1 μs of duration for the protein ubiquitin. We also studied the convergence of the NMR-derived parameters extracted from the MD trajectories in function of their duration. [...] In chapter 6, we addressed the question of the correlation between the motions of the side chains and main chain of a protein. [...] In the first part of the final chapter of the present thesis, we investigated the evolution of the correlation between the side-chain and the main-chain motions of a protein during unfolding/folding events. In this preliminary work, we used a single MD simulation of the ultrafast folder Trp-cage performed at 380 K. We confirmed the results found for proteins in theirnative state. We observed an increase of the correlation between the two time series yn(t) and δn(t) during an unfolding event characterized, here, by the exit of the TRP residue of its “cage”.A steric parameter s was also defined in order to quantify interactions of the amino-acid side chainwith its environment. In a second part of the last chapter, we present a preliminary study of theunfolding of the downhill folder gpW under a mechanical force. To characterized the unfolding ofgpW, we computed the chemical shift of the Cª and of the Hⁿ atoms along the amino-acidsequence of the protein in function of a reaction coordinate: the distance, rCªCª , between the Cª atoms of the N and C terminal residues. We demonstrated that it is hard to distinguish a typical behavior of all the chemical shift of all the residues along the amino-acid sequence in function of the distance rCªCª . However, by averaging the chemical shift over all the residues of the protein we found that the evolution of the average value of the chemical shift described the unfolding eventsof the protein during the MD simulations
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Clements, Joseph Shelby II. "Synthesis of Insecticidal Mono- and Diacylhydrazines for Disruption of K+ Voltage-Gated Channels, and Elucidation of Regiochemistry and Conformational Isomerism by NMR Spectroscopy and Computation." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/77918.

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Based on the success of diacyl-tert-butylhydrazines RH-5849 and RH-1266 in controlling agricultural crop pests, we endeavored to synthesize our own diacylbenzyl- and arylhydrazine derivatives for use against the malaria vector Anopheles gambiae. In the process of producing a library of compounds for assay against An. gambiae, it became clear that employing regioselective acylation techniques (in molecules that feature two nucleophilic, acyclic nitrogen atoms α to one another) would be imperative. Synthesis of the library derivatives proceeded rapidly and after topical assay, we found three compounds that were more toxic than the RH-series leads. One of the three displayed an LD50 value of half that of RH-1266, though patch clamp assay concluded that toxicity was not necessarily linked to inhibition of mosquito K+ channel Kv2.1. The acylation of monoarylhydrazines appears simple, but its regioselectivity is poorly understood when assumed as a function of basicity correlating to nucleophilic strength. We determined the ratio of the rate constants for distal to proximal N-acylation using 19F NMR spectroscopic analysis of reactions of 4-fluorophenylhydrazine with limiting (0.2 equiv) acylating agent in the presence of various bases. Acid anhydrides gave consistent preference for distal acylation. The selectivity of acylation by acyl chlorides when using pyridine gives strong distal preference, whereas use of triethylamine or aqueous base in conjunction with aroyl chlorides showed a moderate preference for proximal acylation. This observation yielded a convenient one-step method to synthesize proximal aroylarylhydrazines in yields comparable or superior to that provided by the standard three-step literature approach. Combined with NMR evidence of the distal nitrogen as the unambigiously stronger base of the two nitrogens, we propose a single electron transfer mechanism that predicts the regiochemistry of arylhydrazines toward acylating agents better than the nucleophilicity model based on pKa values. While synthesizing the acylhydrazine library for assay against An. gambiae, NMR spectroscopy revealed rotational isomerisms of two types: chiral helicity (M)/(P) and acyl (E)/(Z)-isomerism due to hindered rotation. Variable temperature NMR allowed the measurement of N-N bond rotational barriers, as well as estimate the barrier of (E)/(Z) interconversion. We obtained the X-ray crystal structures of four diacylhydrazines to test this hypothesis and revealed both the twist conformation around the N-N bond axis and (E)/(Z)-isomerism around the proximal acyl group. Computation (which agreed with the crystal structures) allowed us to estimate which (E)/(Z)-isomers were most likely being observed in solution at room temperature by NMR spectroscopy. In addition, we were able to calculate transition structures corresponding to N-N bond rotational barriers of (E,Z)- and (Z,Z)-isomers of model molecules and rationalize the difference in coalescence temperatures between (E,Z)- and (Z,Z)-isomers.
Ph. D.
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Rasolofonjatovo, Evelia. "Conception, synthèse et évaluation biologique d’ analogues contraints de l’isocombrétastatine a-4 à visée antitumorale." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA114852.

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Les résistances aux traitements actuels contre le cancer imposent de trouver de nouvelles cibles thérapeutiques. Une de ces cibles est le réseau vasculaire assurant un apport suffisant en nutriments et en oxygène à la tumeur, et permettant l’apparition de métastases. Détruire la vascularisation de la tumeur par l’utilisation d’agents antivasculaires (VDA)revient à l’asphyxier et à l’affamer, inhibant ainsi la prolifération des cellules tumorales et empêchant le processus métastatique. L’objectif de ce travail de thèse a été d’étudier des analogues contraints de l’isocombrétastatine A-4 (isoCA-4), une molécule phare du laboratoire, ayant un excellent pouvoir d’inhibition de la polymérisation de la tubuline et présentant une activité antivasculaire. Ces structures dont la double liaison est incluse dans différents types de cycles C,ont été étudiées également afin d’évaluer l’influence de l’angle dièdre formé par les noyaux A et B sur les activités biologiques des divers types de structures. Préalablement sélectionnés par modélisation moléculaire, ces analogues contraints sont de type 1-arylnaphtalène, 5-arylbenzoxépine ou 4-arylchromène et ont été préparés par des voies d’ accès originales développées dans le cadre de cette thèse. Parmi les composés synthétisés, l’analogue de type benzoxépine 3-53est aussi cytotoxique que l’isoCA-4 et possède un pouvoir d’inhibition de la polymérisation de la tubuline équivalent. Une évaluation plus poussée de son profil biologique, ainsi que celle des meilleurs représentants de chaque série chimique est actuellement en cours
Most tumor cells rely on an efficient vascular supply for their survival, making the tumor vasculature an attractive target for anti-cancer therapy. This thesis aimed at the design and synthesis of constrained analogues of isocombretastatin A-4(isoCA-4), an antivascular agent developed in the laboratory, which exerts excellent cytotoxicities against a large panel ofcancer cell lines, and strongly inhibits tubulin polymerization. Conformationally restricted analogues of isoCA-4,featuring 1-arylnaphthalene, 5-arylbenzoxepine or 4-arylchromene skeletons were designed by computational studies andprepared by novel synthetic strategies. Of all synthesized compounds, benzoxepine analogue 3-53 strongly inhibits tubulinpolymerization and shows excellent cytotoxicities against several human cancer cell lines
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TSAI, Jie-Sung, and 蔡杰松. "Recognition of Protein α-helices and β-sheets with Dihedral Angles." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/15037125687227883656.

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碩士
國立中興大學
資訊科學系所
94
The prediction of the protein secondary structure helps biologists to evaluate the similarities between proteins with unknown 3D structures and those proteins with known 3D structures. In this study, we propose a new method based on dihedral angle vectors to recognize the regions of α-helices and β-sheets. First, we assume that the information of secondary structure of a protein could be conserved in the dihedral angle vectors of consecutive secondary structure sequences. And then, we apply the clustering method on the sets of dihedral angel vectors to gather groups of vectors which have characteristics of similar 3D structures. In the end, we use the obtained results from the clustering method to construct the scoring matrix of peptide segments connecting with the relationships between the primary and secondary structure sequences of the non-redundant dataset of PDB. Our method provides not only the predictor of α-helices and β-sheets but also the given level of confidence on each position of a testing protein. Moreover, the predictor reveals information about the secondary structure supported by a particular scoring matrix; that is, the predictor provides information about the rules of primary sequences to form the secondary structure. In contrast, predictors that use neural network or support vector machine to construct the prediction models only provide prediction of 3-state protein secondary structure.
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Kuo, Nei-Jing, and 郭乃菁. "An Automatic Classification of Dihedral Angle Regions Using Structures-Based Profiles." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/72314111952893958907.

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碩士
逢甲大學
資訊工程所
98
Two of the well known protein, Φ and Ψ, values pair are usually plotted in a Ramachandran plot. And the concentrated areas in the plot, defined as dihedral angle regions, are known highly correlated to protein secondary structures. In recent studies, accurate prediction of protein dihedral angle regions was reported to be improved by using sequence-based and structure-based information as input features. As we know high sequence similarity of two proteins does not imply the same relationship of structural similarity. Therefore, take more structure information into account is necessary in this research. The structural-based profile is a scoring matrix of the statistical probability distribution from local structure descriptor where it can be any structure related properties, such as other well defined torsion angles (KAPPA, ALPHA, TCO), structure elements (DSSP, HMMSTR, STR, PB) and accessible solvent areas (ASA). We present a method that applied support vector machine (SVM) algorithm to predict the dihedral angle regions of residues using Position Specific Score Matrix (PSSM) profile and structure-based profiles. We trained on a benchmark of 150 proteins in our approach leads to dihedral angle region predictions, that accuracy achieved 75% only using one of structure-based profiles. And we integrated the sequence-based profile with the structure-based profiles to predict dihedral angle regions and the accuracy achieve 77%. It’s obvious the use of the plentiful structure-based profiles help improving the dihedral angle regions prediction.
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Heng-TengChen and 陳恆燈. "Analysis and Discussion on Efficiency of Applying Dihedral Angle to Multi-rotor UAV." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/692p29.

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碩士
國立成功大學
航空太空工程學系
106
This research adopted dihedral angles for quadcopter design. A dihedral angle design could assist attitude subsystem to suppress its maximum overshoot, hence minimizes the body swing. According to the experiment conducted in this research, a dihedral angle design could reduce up to 24% of maximum overshoot. In this research, the advantages of a dihedral angle design is evaluated, and then calculate the state estimation of a standard quadcopter and quadcopters with different dihedral designs. Find the control target by deriving the Dynamic Equations. An experiment is conducted to verify the theory, using a quadcopter with different dihedral angle design modules. According to control theory and its simulation result, a dihedral angle design is similar to adding a damper on quadcopter system, and could reduce the maximum overshoot. This result not only shows that a dihedral angel design could reduce the maximum overshoot, but also finds out the trend among different dihedral angles and their maximum overshoot with statistic methods. Furthermore, dihedral angle designs could also reduce swing and stop the swing earlier. One other thing worth mentioning is that the power efficient is better than expectation. This research has high commercial value, and its result could be applied to those tasks which require higher precision, such as aerial photography, industrial inspection, etc. In order to have a thorough look into dihedral angel designs, a further research regarding power consumption and the algorithm of flight control system is recommended.
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Chen, Bo-Jian, and 陳柏堅. "Analysis of the Blade Dihedral Angle on the Power Output Effect of the Wind Turbine." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/56200011635781843311.

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碩士
國立屏東科技大學
機械工程系所
96
This research studies the effects of blade dihedral angle on the power output of a horizontal axis wind turbine. The purpose is to adjust the dihedral angle to reduce the power output of the blades, such that preventing damage the electric generator from over-speed the system. Both the blade element theory and momentum theory are used to develop the 3-dimensional blade shape, and then the Computational Fluid Dynamics (C.F.D.) method is introduced to resolve the flow-field details, and evaluate the performance of the system. The 3-dimensional blade shape is submitted to a mesh generator, GAMBIT, to create the mesh for the flow solver, which is FLUENT. NACA4415 airfoil is used for the blade sections. Various dihedral angles are used to make a map to determine the suitable angle that can make the wind turbine delivers the rated-power at a specified wind speed which is higher then the rated-wind speed. The results showed that the dihedral angle required at wind speed of 10 m/s is about 20°, at 11 m/s is about 25°, and at 12 m/s is about 30°. Therefore, the model of adjusting the output power by regulate the turbine blade dihedral angle suggested in this work is proved feasible.
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Altis, Alexandros [Verfasser]. "Modeling the free energy landscape of biomolecules via dihedral angle principal component analysis of molecular dynamics simulations / von Alexandros Altis." 2008. http://d-nb.info/993966969/34.

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Begay, Shanadeen Crystal. "Thermodynamics and structure of methionine enkephalin using the statistical temperature molecular dynamics algorithm." Thesis, 2015. https://hdl.handle.net/2144/15704.

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Kim, Straub, and Keyes introduced the statistical temperature molecular dynamics (STMD) algorithm to overcome broken ergodicity by sampling a non­-Boltzmann flat energy histogram as noted in Kim, Straub, and Keyes, Phys. Rev. Lett. 97: 050601 (2007). Canonical averages are calculated via reweighting to the desired temperature. While STMD is promising, its application has been almost entirely to simple or model systems. In this dissertation the implementation of STMD into the biosimulation package CHARMM is used to simulate the methionine enkephalin pentamer peptide with a methione terminal cap in a droplet of CHARMM TIP3P water molecules. Chain thermodynamics is analyzed from the novel perspective of the statistical temperature as a function of potential energy, $TS(U), automatically generated by STMD. Both the minimum in the slope of $TS(U), and the peak in the heat capacity as a function of temperature, calculated via reweighting, indicate a collapse transition at Tθ ≈ 253K. Distributions of dihedral angles are obtained as a function of temperature. Rotamer regions found in the literature are reproduced, along with unique regions not found previously, including with advanced algorithms, indicating the power of STMD enhanced sampling.
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Books on the topic "Dihedral angles"

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M, Ware George, and Langley Research Center, eds. Control effectiveness and tip-fin dihedral effects for the HL-20 lifting-body configuration at Mach numbers from 1.6 to 4.5. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1995.

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Book chapters on the topic "Dihedral angles"

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Souza, Michael, Carlile Lavor, and Rafael Alves. "Modeling the Molecular Distance Geometry Problem Using Dihedral Angles." In Bioinformatics Research and Applications, 270–78. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-59575-7_24.

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Cui, Xuefeng, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, and Ming Li. "How Accurately Can We Model Protein Structures with Dihedral Angles?" In Lecture Notes in Computer Science, 274–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-33122-0_22.

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Ley-Koo, Eugenio, and Guo-Hua Sun. "Surface Effects in the Hydrogen Atom Confined by Dihedral Angles." In Electronic Structure of Quantum Confined Atoms and Molecules, 1–29. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-09982-8_1.

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Abouelaziz, Ilyass, Mohammed El Hassouni, and Hocine Cherifi. "No-Reference 3D Mesh Quality Assessment Based on Dihedral Angles Model and Support Vector Regression." In Lecture Notes in Computer Science, 369–77. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-33618-3_37.

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Zimmermann, Olav. "Backbone Dihedral Angle Prediction." In Methods in Molecular Biology, 65–82. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6406-2_7.

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Diez, Mikel, Victor Petuya, Mónica Urizar, and Alfonso Hernández. "Protein Folding Pathways Implementing Dihedral Angle Variable Speed." In Latest Advances in Robot Kinematics, 277–84. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4620-6_35.

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Diez, Mikel, Víctor Petuya, Imanol Martínez, and Alfonso Hernández. "Protein Secondary Structure Detection Using Dihedral Angle Parameters Evaluation." In The 11th IFToMM International Symposium on Science of Mechanisms and Machines, 127–34. Cham: Springer International Publishing, 2013. http://dx.doi.org/10.1007/978-3-319-01845-4_13.

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Faraggi, Eshel, and Andrzej Kloczkowski. "Protein Secondary Structure Assignments and Their Usefulness for Dihedral Angle Prediction." In Springer Series on Bio- and Neurosystems, 699–712. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-95843-9_21.

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Diez, M., V. Petuya, M. Urizar, E. Macho, and O. Altuzarra. "Computation of the Protein Molecular Mechanism Using Adaptive Dihedral Angle Increments." In New Trends in Mechanism and Machine Science, 105–12. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4902-3_11.

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Kurochkina, Natalya A., Hong Seok Kang, and B. Lee. "Experiences with Dihedral Angle Space Monte Carlo Search for Small Protein Structures." In NATO ASI Series, 147–57. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4899-1349-4_14.

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Conference papers on the topic "Dihedral angles"

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Subramanian, Raghavendran, and Kazem Kazerounian. "Residue Level Inverse Kinematics of Peptide Chains in the Presence of Observation Inaccuracies and Bond Length Changes." In ASME 2005 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2005. http://dx.doi.org/10.1115/detc2005-84352.

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Dihedral angles as generalized coordinates define the geometric conformation of a peptide chain. Given the exact coordinates of the atoms, it is possible to rigorously calculate the dihedral angles. We will refer to this calculation process as the residue level inverse kinematics of peptide chains. However uncertainties and experimental observation inaccuracies in the atoms’ coordinates handicap this otherwise simple and straightforward process. In this paper, we present three new efficient methodologies to find all the dihedral angles of a peptide chain for a given conformation. Comparison of these results with the dihedral angle values reported in the PDB (Protein Data Bank) indicates significant improvements. While these improvements benefit most modeling methods in protein analysis, it is in particular, very significant in homology modeling where the dihedral angles are the structural variables. The first method presented here fits a best plane through five atoms of each peptide unit. The angle between the successive planes is defined as the dihedral angle. The second method is based on the Zero-Position analysis method. Successive links in this method rotate by the dihedral angles so as to minimize the structural error between respective atoms in the model conformation with given atoms’ coordinates. Dihedral angle final values correspond to the minimum structural error configuration. In this method, singular value decomposition (SVD) technique is used to best fit the atoms in the two conformations. The third method is a variant of the second method. In this instead of rotating all the links successively only three links are matched each time to extract the dihedral angle of the middle link. By doing so, the error accumulation on the successive links is reduced. This paper focuses on the Euclidean norm as the measure of merit (structural error) to compare different methods with the Protein Data Bank (PDB). This Euclidean norm is further, minimized by optimizing the geometrical features of the peptide plane.
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Musa, Nur Amalina, Shuhaimi Mansor, Airi Ali, and Mohd Hasrizam Che Man. "Effect of Tail Dihedral Angle on Lateral Directional Stability due to Sideslip Angles." In 53rd AIAA Aerospace Sciences Meeting. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2015. http://dx.doi.org/10.2514/6.2015-1498.

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Xing, David, and Zhong You. "Constructing Scissor-Like Structures and Parallelogram Linkages With 4-Crease Single-Vertex Flat-Foldable Rigid Origami and Their Thick-Panel Versions." In ASME 2019 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/detc2019-97983.

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Abstract Scissor-like structures are commonly composed of two straight rigid supports in a crisscross pattern connected by a pivot at its point of intersection [1]. Opposite angles formed by the supports are equal regardless of the structure’s folded state. Parallelogram linkages have a similar property. Rigid origami can be used to create these structures by combining two identical copies of a 4-crease single-vertex flat-foldable rigid origami, a single 4C, to form a flat-foldable composite structure, a double 4C. In this paper, we prove mathematically that regardless of the folded state of a single-4C, its even dihedral angles are equal, and odd dihedral angles are equal. As a result, the double 4C consists of 2 scissor-like structures. A past method to prove these dihedral angle equalities requires a more complex approach involving rotation matrices using Denavit and Hartenberg parameters [2,3]. This paper will provide a more intuitive method that proves the same equalities. We will also show that a similar construction of the double 4C using thick-panel versions of the single 4C satisfies the same dihedral angle equalities necessary for the formation of parallelogram linkages. The construction of the double 4C can help design self-folding mechanisms and useful metamaterials.
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Herndon, Joshua, and Sumi Singh. "Protein structural domain prediction based on dihedral and geometric angles." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8218012.

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Dong, Qiwen, Xin Geng, Shuigeng Zhou, and Jihong Guan. "Empirical Probability Functions Derived from Dihedral Angles for Protein Structure Prediction." In 2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering (BIBE). IEEE, 2009. http://dx.doi.org/10.1109/bibe.2009.55.

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Roy, Bhaskar, P. A. Laxmiprasanna, Vishal Borikar, and Amit Batra. "Low Speed Studies of Sweep and Dihedral Effects on Compressor Cascades." In ASME Turbo Expo 2002: Power for Land, Sea, and Air. ASMEDC, 2002. http://dx.doi.org/10.1115/gt2002-30441.

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The use of three dimensional blade designs incorporating end bend, sweep and dihedral to reduce secondary flow related losses, improve efficiency and stable operating range has gained ground in the recent years. In the present study a straight cascade, a swept cascade, and a dihedral cascade have been considered. Effects of sweep and dihedral along the span are studied at 0° and +20° stagger. The study shows that both the sweep and the dihedral have lower end-wall losses compared to the straight cascade. However, lower losses are accompanied with lower diffusion factors. At mid-span also the lowering of losses is achieved along with some lowering of diffusion factor. While the dihedral seems to contribute for stable operation more near the end-wall, the swept blade contributes more near the mid-span. The swept blade is able to sustain the flow at higher angles of attack. While the end-wall loss benefits are welcome with lower loading, at mid-span lower loading obtained may need to be corrected by increasing the design angle of incidence.
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Fei, Teng, Lucheng Ji, and Weilin Yi. "Investigation of the Dihedral Angle Effect on the Boundary Layer Development Using Special-Shaped Expansion Pipes." In ASME Turbo Expo 2018: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/gt2018-76383.

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The corners between the blades and end walls are common geometric structures in turbomachinery, where boundary layers on the blade and end wall surface interact with each other. This boundary layer interaction enlarges the region of low momentum fluid which leads to the boundary layers grow thicker at the corner region. Then the corner separation is likely to occur, and even worse by the adverse pressure gradient along the streamwise as well as secondary flows along the pitchwise. The key issue to design the geometric structures of the corner region is to control the dihedral angle between the blade and end wall surface. However, from the current published literature, few researchers have studied the influence of dihedral angle on the flow structures at the corner region in detail. In this paper, a series of expansion pipes with different cross sections which represent different dihedral angles are simulated. Then, some useful conclusions about how the dihedral angle affects the flow structures at the corner region are drawn. Moreover, a new method to predict the boundary layer thickness at the corner region is introduced, and the predicted results are in good agreement with simulation results.
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Miklosovic, D. S., and P. M. Bookey. "An Analytic and Experimental Investigation of the Aerodynamic Performance Enhancements of Multiple Winglet Configurations." In ASME 2005 Fluids Engineering Division Summer Meeting. ASMEDC, 2005. http://dx.doi.org/10.1115/fedsm2005-77255.

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An experimental effort was undertaken to assess the effectiveness and efficiency of three winglets mounted chordwise to the tip of a rectangular wing (NACA 0018 section). The winglets, with an aspect ratio of 3.6, were mounted on a half-span wing having an aspect ratio of 3.1. Twenty configurations of varying dihedral arrangements were analyzed with a vortex lattice method and tested in a low-speed wind tunnel at a Reynolds number of 600,000. In general, the arrangements involving high dihedral angles had lower performance increments, due to lower lift and higher interference drag. More specifically, the results showed that the winglets placed at 60, 45, and 30 degrees, respectively, produced nominal 4% higher lift and 46% lower drag. The most dramatic findings from this study show that positioning the winglet dihedral angles had the result of adjusting the point of maximum L/D and the magnitude of the pitching moment coefficient. These observations suggest that multiple winglet dihedral changes affect the lift, drag, and pitching moment in such a way that they are feasible for use as actively-controlled surfaces to improve the performance of aircraft at various flight conditions and to “tune” the longitudinal stability characteristics of the wing.
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Petrova, Dobrinka. "Protein structure comparison based on distances between secondary structure elements and backbone dihedral angles." In the 12th International Conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2023607.2023668.

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Subramanian, Raghavendran, and Kazem Kazerounian. "Improved Molecular Model of a Peptide Unit for Proteins." In ASME 2006 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2006. http://dx.doi.org/10.1115/detc2006-99315.

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Pauling, Corey and Branson in their seminal paper in 1951 reported numerical values for the bond lengths and bond angles for a peptide unit in proteins. These values became the standard model for several decades after that. This classic peptide model was either confirmed or improved upon by other researchers over the years, by using more advanced X-Ray diffraction equipments. In this paper, we have made an attempt to calibrate the values of these bond lengths and bond angles based on a systematic and deterministic approach applied to a collection of proteins defined structurally in the Protein Data Bank (PDB). Our method is based on the assumption that a peptide chain is a serial chain of identical rigid bodies connected by revolute joints (i.e. dihedral angles). The proposed procedure first computes the best estimate for the dihedral angles in the presence of inaccuracies in the atoms’ coordinates data. Then these values are used to find the conformation of the peptide chain using the calibrated model of the peptide unit. Through an optimization process, the structural error (RMSD of all atoms) between the resultant conformation and the PDB data is minimized to yield the best values for the bond length and bond angles in the calibrated peptide unit. Our numerical experiments indicate that by making small changes in the Pauling-Corey peptide model parameters (0.15% to 8.7%) the structural error is reduced significantly (3.0% to 57.4%). The optimum values for the bond angles and bond lengths are as follow: Bond Lengths: N-C(A): 1.4721Å, C(A)-C: 1.6167Å, C-N: 1.2047Å, C=O: 1.1913Å and N-H: 0.9621Å. Bond Bending Angles: N-C(A)-C: 109.6823°, C(A)-C=0: 119.518°, C(A)-C-N: 114.5553°, O=C-N: 125.9233°, C-N-H: 123.5155°, C-N-C(A): 121.5756°, C(A)-N-H: 114.901°. Peptide bond torsion angle: ω: 179.4432°.
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Reports on the topic "Dihedral angles"

1

Verly, J. G. Physical Optics Polarization Scattering Matrix for a Right-Angle Dihedral. Fort Belvoir, VA: Defense Technical Information Center, February 1995. http://dx.doi.org/10.21236/ada293036.

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