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Da, Ronch Andrea. "On the calculation of dynamic derivatives using computational fluid dynamics." Thesis, University of Liverpool, 2012. http://livrepository.liverpool.ac.uk/5513/.
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In this thesis, the exploitation of computational fluid dynamics (CFD) methods for the flight dynamics of manoeuvring aircraft is investigated. It is demonstrated that CFD can now be used in a reasonably routine fashion to generate stability and control databases. Different strategies to create CFD-derived simulation models across the flight envelope are explored, ranging from combined low-fidelity/high-fidelity methods to reduced-order modelling. For the representation of the unsteady aerodynamic loads, a model based on aerodynamic derivatives is considered. Static contributions are obtained from steady-state CFD calculations in a routine manner. To more fully account for the aircraft motion, dynamic derivatives are used to update the steady-state predictions with additional contributions. These terms are extracted from small-amplitude oscillatory tests. The numerical simulation of the flow around a moving airframe for the prediction of dynamic derivatives is a computationally expensive task. Results presented are in good agreement with available experimental data for complex geometries. A generic fighter configuration and a transonic cruiser wind tunnel model are the test cases. In the presence of aerodynamic non-linearities, dynamic derivatives exhibit significant dependency on flow and motion parameters, which cannot be reconciled with the model formulation. An approach to evaluate the sensitivity of the non-linear flight simulation model to variations in dynamic derivatives is described. The use of reduced models, based on the manipulation of the full-order model to reduce the cost of calculations, is discussed for the fast prediction of dynamic derivatives. A linearized solution of the unsteady problem, with an attendant loss of generality, is inadequate for studies of flight dynamics because the aircraft may experience large excursions from the reference point. The harmonic balance technique, which approximates the flow solution in a Fourier series sense, retains a more general validity. The model truncation, resolving only a small subset of frequencies typically restricted to include one Fourier mode at the frequency at which dynamic derivatives are desired, provides accurate predictions over a range of two- and three-dimensional test cases. While retaining the high fidelity of the full-order model, the cost of calculations is a fraction of the cost for solving the original unsteady problem. An important consideration is the limitation of the conventional model based on aerodynamic derivatives when applied to conditions of practical interest (transonic speeds and high angles of attack). There is a definite need for models with more realism to be used in flight dynamics. To address this demand, various reduced models based on system-identification methods are investigated for a model case. A non-linear model based on aerodynamic derivatives, a multi-input discrete-time Volterra model, a surrogate-based recurrence-framework model, linear indicial functions and radial basis functions trained with neural networks are evaluated. For the flow conditions considered, predictions based on the conventional model are the least accurate. While requiring similar computational resources, improved predictions are achieved using the alternative models investigated. Furthermore, an approach for the automatic generation of aerodynamic tables using CFD is described. To efficiently reduce the number of high-fidelity (physics-based) analyses required, a kriging-based surrogate model is used. The framework is applied to a variety of test cases, and it is illustrated that the approach proposed can handle changes in aircraft geometry. The aerodynamic tables can also be used in real-time to fly the aircraft through the database. This is representative of the role played by CFD simulations and the potential impact that high-fidelity analyses might have to reduce overall costs and design cycle time.
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Brown, Kieron David. "Computational analysis of low speed axial flow rotors." Thesis, University of Bristol, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389158.
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Tang, Xiao. "Computational investigation of 2D functional materials for nanoelectronics." Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/206075/1/Xiao_Tang_Thesis.pdf.
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This thesis investigated several new 2D functional materials and explored the feasibility for electronic applications. The first part of this thesis mainly focused on the prediction of new 2D materials that hold great promise for field effect transistors and spintronics. The second part systematically studied the possibilities of ferroelectric switching on magnetism tuning and gas sensing. The exploration of novel 2D materials and associated outstanding electronic/magnetic properties provided a deep understanding for the observed phenomena and paved the foundations for high-performance electronics.
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Almlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.
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The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.
For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.
A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.
A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.
The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.
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Almlöf, Martin. "Computational methods for calculation of Ligand-Receptor binding affinities involving protein and nucleic acid complexes /." Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.
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Fey, Natalie. "Molecular modelling of ferrocenes and arylphosphines." Thesis, Keele University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368982.
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Fosso-Tande, Jacob. "A Computational Chemistry Study of Spin Traps." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etd/2127.
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Many defects in physiological processes are due to free radical damage: reactive oxygen species, nitric oxide, and hydroxyl radicals have been implicated in the parthenogenesis of cancer, diabetes mellitus, and rheumatoid arthritis. We herein characterize the phenyl-N-ter-butyl nitrone (PBN) type spin traps in conjunction with the most studied dimethyl-1-pyrroline-N-oxide (DMPO) type spin traps using the hydroxyl radical. In this study, theoretical calculations are carried out on the two main types of spin traps (DMPO and PBN) at the density functional theory level (DFT). The energies of the optimized structures, hyperfine calculations in gaseous and aqueous phases of the spin traps and the hydroxyl radical adduct are calculated at the B3LYP correlation and at the 6-31G (d) and 6-311G (2df, p) basis sets respectively. The dielectric effect on the performance of the spin trap is determined using the polarized continuum model. Calculations show a localization of spin densities in both cases. However, DMPO spin traps are shown to be more stable and more interactive in aqueous environment.
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Tang, Cheng. "Computational exploration of two-dimensional materials with novel electronic, optical and magnetic properties." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/212532/1/Cheng_Tang_Thesis.pdf.
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This project was a step forward in discovering new two-dimensional (2D) structures for electronic and spintronic applications. This work comprehensively investigates seven intriguing 2D structures with novel electronic, optical and magnetic properties on the basis of the global structural search and first-principles calculations. These findings not only highlight the promising materials platforms for advanced nanodevices but also provide the theoretical guides for designing multifunctional 2D materials.
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Parasuram, Priya Laity John H. "Homologous modeling and structure calculation of the MTF-1 zinc finger domain protein using NMR and computational techniques." Diss., UMK access, 2006.
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Thesis (M.S.)--School of Computing and Engineering. University of Missouri--Kansas City, 2006."A thesis in computer science." Typescript. Advisor: John H. Laity. Vita. Title from "catalog record" of the print edition Description based on contents viewed Nov. 1, 2007. Includes bibliographical references (leaves 81-88). Online version of the print edition.
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Castro, Aguilera Abril Carolina. "Computational study of nuclear magnetic shielding constants." Doctoral thesis, Universitat de Girona, 2017. http://hdl.handle.net/10803/565597.
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Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable structural tool in the modern analytical arsenal of chemists and structural biologists. The present thesis is a computational study of the NMR shift constants in a number of chemical systems of interest, using both static and dynamic approaches via Density Functional Theory, to predict, confirm the presence of transient species, and/or explain ambiguous signals in the NMR spectra. Special attention was put on cases where there are strong interactions between the solvent and the molecule studied. In addition, this thesis addresses other methodological issues that influence the quality of the calculated NMR chemical shifts such as the level of theory, the explicit inclusion of solvent molecules, the choice of the reference molecule, as well as the relativistic effects for heavy element compoundsL’espectroscòpia de Ressonància Magnètica Nuclear (RMN) és una eina indispensable en el modern arsenal de químics analítics i biòlegs estructurals.La present tesi és un estudi computacional dels desplaçaments químics de RMN en un nombre de compostos químics d’interès, usant aproximacions estàtiques i dinàmiques mitjançant la teoria del funcional de la densitat, la qual ajudarà a predir, a confirmar i/o a complementar dades obtingudes experimentalment. S’ha donat especial atenció en casos on existeixen fortes interaccions substrat-solvent. Addicionalment, aquesta tesi aborda altres problemes metodològics que afecten la qualitat dels desplaçaments químics teòrics com el nivell de teoria, la inclusió explícita de molècules de solvent, l’elecció de la molècula de referència, així com els efectes relativistes en compostos que contenen àtoms pesats
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De, Pietri Marco. "Development of a Human Unstructured Mesh Model Based on CT Scans for Dose Calculation in Medical Radiotherapy." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017.
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Questo lavoro di tesi analizza l’opportunità di applicare dei metodi Monte Carlo nei campi della Radioterapia Superficiale e Ortovoltaica. Inizialmente i protocolli di cura attualmente esistenti sono stati studiati. Una revisione della letteratura è stata condotta sulle tipologie ed evoluzione dei fantocci umani computazionali. I passaggi pratici per la realizzazione di due tipi di fantocci basati su paziente, partendo da immagini TAC, sono stati descritti. Questi due tipi, modelli voxel e modelli a mesh non strutturate, sono stati studiati e comparati attraverso simulazioni. Dalla collaborazione con il reparto di Fisica Medica dell’Arcispedale S. Maria Nuova di Reggio Emilia, un modello di un tubo a Raggi X è stato modellato e validato con misure sperimentali. Questa sorgente è stata utilizzata su fantocci di teste attraverso simulazioni con MCNP6. In particolare è stata valutata la distribuzione spaziale della dose, dentro al modello, a tensioni crescenti all’interno del tubo. Il confronto dei risultati delle simulazioni ha permesso di valutare le interazioni dei fotoni all’interno del modello e le dosi al Planning Target Volume (PTV) e Organ At Risk (OAR) a tensioni della sorgente crescenti. Queste applicazioni hanno dimostrato che un prototipo di Sistema di Piano di Trattamento (TPS) è facilmente implementabile e può fornire preziose informazioni aggiuntive su questi tipi di radioterapia. Sebbene i protocolli esistenti siano in uso da molti anni, con innegabili tassi di cura elevati, è opinione dell’autore che l’integrazione di un TPS basato su Monte Carlo possa fornire potenziali benefici a questi tipi di radioterapia. In particolare, potrebbe fornire informazioni aggiuntive sulla scelta dei parametri di trattamento, portando a migliori risultati nella terapia e qualità di vita del paziente oncologico.
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Popov, G. F., S. I. Savan, R. V. Lazurik, and A. V. Pochynok. "Selection of calculation methods for the analysis of absorbed depth-dose distributions of electron beams." Thesis, Sumy State University, 2016. http://essuir.sumdu.edu.ua/handle/123456789/46936.
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The work is dedicated to comparison methods of processing the results of measurements of the absorbed depth-dose distributions (DDD) of the electron radiation to determine the practical range of electrons. The sets of test data were obtained by modeling the DDD with use Monte Carlo method. The accuracy of the calculation method is determined by the mean square error of processing results the sets of test data. In the paper it was performed the comparison of computational methods of processing the measurement results that differs in the sizes of the array of data being processed and types of functions which use for approximation the data. Comparison the accuracy methods is base for the recommendations on the selection of computational methods for determining the practical range of electrons for computational dosimetry of electron radiation.
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Machat, Mohamed. "Computational geometry for the determination of biomolecular structures." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066359/document.
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En bioinformatique structurale, une partie des méthodes computationnelles qui calculent les structures de protéines à l'aide de données expérimentales, effectuent une optimisation de la position des atomes sous les contraintes expérimentales mesurées sur le système étudié, ainsi que sous des contraintes provenant de la connaissance générique de la stéréochimie organique. Ces méthodes d'optimisation présentent l'inconvénient de ne pas garantir la détermination de la meilleure solution. De plus, la validation de l'optimisation se fait en comparant les résultats obtenus pour des calculs répétés, et le résultat d'un calcul est accepté dans la mesure où le même résultat est obtenu plusieurs fois. Par cette approche, on rend plus difficile la détection de conformations alternatives de protéines, qui sont pourtant le sujet d'un vif intérêt dans la littérature. En effet, le développement de la sensibilité des techniques de résonance magnétique nucléaire (RMN) a permis de mettre en évidence plusieurs cas d'échange conformationnel reliés à la fonction des protéines. Dans ce projet de thèse, nous avons étudié une nouvelle approche pour le calcul de structures des protéines et l'exploration de leurs espaces conformationnels, basée sur la résolution du problème de Géométrie de Distance associé aux contraintes de distances dans une protéine par l'algorithme "interval Branch and Prune". Le logiciel implémentant cette méthode est appelée iBPprot, il incarne l'une des premières tentatives d'échantillonnage exhaustive des espaces conformationnels des protéines. Dans un premier temps, on s'est intéressé à l'application de la méthode en utilisant exclusivement des constraintes de distances exactes. Les résultats ont démontré que iBPprot était capable de reconstruire des structures références en s'appuyant seulement sur quelques contraintes à courte portée. De plus, la reconstruction a été d'une précision telle que la conformation générée présentait un RMSD de 1 Angstrom maximum avec la structure référence. L'exploration exhaustive de l'espace conformationnel a été possible pour une bonne partie des protéines cibles. Les temps de calcul pour l'exploration des espaces conformationnels ont été très variables allant de quelques secondes pour quelques protéines jusqu'à des semaines pour d'autres. L'évaluation de la qualité des structures obtenues a démontré qu'au moins 68% des valeurs de phi et psi sont localisées dans la zone 'core' du diagramme de Ramachandran. Cependant, des clash stériques ont été détectées dans plusieurs conformations mettant en jeu jusqu'à 7% d'atomes dans quelques unes de ces conformations. Dans un deuxième temps, on s'est intéressé à l'application de la méthode en incluant des intervalles de distances comme contraintes dans les calculs. Dans ce cas de figure, la méthode a réussi a reconstruire des structures références avec un RMSD inférieur à 5 Angstrom pour plus de la moitié des protéines cibles. En contre partie, le parcours complet de l'espace conformationnel n'a été possible que pour la plus petite protéine de l'ensemble des protéines étudiées. Pour la moitié des autres protéines, plus de 70% des atomes ont vu leurs positions échantillonnées. La qualité des structures obtenues a regressé en comparaison avec les simulations faites avec des distances exactes. En effet, seulement 53% des valeurs de phi et psi étaient localisées dans la zone 'core' du diagramme de Ramachandran, et le pourcentage d'atomes impliqués dans un clash stérique s'élevait jusqu'à 22% pour quelques protéines. Concernant le temps de calcul, le taux de génération de conformations a été déterminé pour chaque protéine cible, et il s'est avéré que globalement sa valeur etait compétitive par rapport aux valeurs des taux observables dans la littératureStructural biology has allowed us expand our knowledge of living organisms. It is defined as the investigation of the structure and function of biological systems at the molecular level. Studying a biomolecule's structure offers insight into its geometry, as angles and distances between the biomolecule's atoms are measured in order to determine the biomolecular structure. The values of these geometrical parameters may be obtained from biophysical techniques, such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. One of the most used methods to calculate protein structures from geometric restraints is simulated annealing. This method does not guarantee an exhaustive sampling of protein conformational space, which is a shortcoming as one protein may adopt multiple functional conformations, and it is important to determine them exhaustively. In this PhD project, the efficiency of a new method - derived from operations research and computational geometry - is studied in order to answer this question: How does this method explore the conformational spaces of small proteins? This method - implemented within the iBPprot software framework - treats protein structure determination as a distance geometry problem, which the interval branch-and-prune algorithm tries to solve by the full exploration of its solutions space. The results obtained by iBPprot on a set of test proteins, with sizes ranging from 24 to 120 residues and with known structures, are analyzed here. Using short-range exact distance restraints, it was possible to rebuild the structure of all protein targets, and for many of them it was possible to exhaustively explore their conformational spaces. In practice, it is not always possible to obtain exact distance restraints from experiments. Therefore, this method was then tested with interval data restraints. In these cases, iBPprot permitted the sampling of the positions of more than 70% of the atoms constituting the protein backbone for most of the targets. Furthermore, conformations whose r.m.s. deviations closer than 6 Angstrom to the target ones were obtained during the conformational space exploration. The quality of the generated structures was satisfactory with respect to Ramachandran plots, but needs improvement because of the presence of steric clashes in some conformers. The runtime for most performed calculations was competitive with existing structure determination method
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He, Peng. "FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/531465.
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ChemistryPh.D.
Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics.
Temple University--Theses
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Souza, Kleymilson do Nascimento. "Optimization in calculation of active part three phase distribution transformer with use genetic algorithms aiming better efficiency and less cost." Universidade Federal do CearÃ, 2012. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=8364.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel SuperiorThe present work is a study of a methodology that seeks to be more economical and efficient compared to traditional methods, the design of three phase distribution transformers. To this end, we use a tool of Computational Intelligence, based on previous calculations made in the traditional way by manufacturing industries and books that address this matter. It is evident here, another way to design the active part of the transformer, the dimension of the core and coil, for this, used Genetic Algorithms (GA) which will assist in the calculation and selection of parameters, providing the best choice of design of the transformer, minimizing, on average, 5% in the cost and losses in 2.5% as input parameters the following standard. With changes in the fitness function of GA, one can simply adapt to new requirements and standards. As a result of using the genetic algorithm can find a design solution that is more efficient than that used by the manufacturers. The losses calculated values meet established by NBR-5440.
O presente trabalho faz um estudo de uma metodologia que busca ser mais econÃmica e eficiente, em comparaÃÃo com mÃtodos tradicionais, no projeto de transformadores de distribuiÃÃo trifÃsico. Para tal, utiliza-se uma ferramenta de InteligÃncia Computacional, tendo como base cÃlculos anteriores feitos de forma tradicional por indÃstrias fabricantes e livros que tratam desse assunto. Evidencia-se, aqui, mais uma maneira de projetar a parte ativa do transformador, ou seja, o dimensionamento do nÃcleo e bobinas; para isso, utiliza-se Algoritmos GenÃticos (GA), que irÃo auxiliar no cÃlculo e escolha dos parÃmetros, proporcionando a melhor escolha do projeto do transformador, minimizando, em mÃdia, o custo em 5 % e as perdas em 2,5 %, conforme parÃmetros de entrada seguindo a norma. Com modificaÃÃes na funÃÃo de fitness do GA, pode-se adequar de maneira simples a novas exigÃncias e normas. Como consequÃncia da utilizaÃÃo do Algoritmo GenÃtico pode-se encontrar uma soluÃÃo de projeto que à mais eficiente do que a utilizada pelos fabricantes. As perdas calculadas atendem valores estabelecidos pela norma NBR-5440.
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Park, In-Hee. "Computational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1276745410.
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Gahm, Märta, and Nedim Velic. "FASTIGHETERS UNDERHÅLLSSKULD : EN STUDIE AV BERÄKNINGSMODELLER FÖR EFTERSATT UNDERHÅLL MED AVSEENDE PÅ OLIKA BYGGNADSTEKNISKA SYSTEM." Thesis, Tekniska Högskolan, Högskolan i Jönköping, JTH, Byggnadsteknik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-29518.
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Altea, Claudinei de Moura. "Computational determination of convective heat transfer and pressure drop coefficients of hydrogenerators ventilation system." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/3/3150/tde-28092016-095253/.
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The objective of the present work is to determinate the pressure drop and the heat transfer coefficients, normally applied to analytical calculations of hydrogenerators thermal design, obtained by applying numerical calculation (Computational Fluid Dynamics - CFD) and validated by experimental results and field measurements. The object of study is limited to the most important region of the ventilation system (the cooling air ducts of stator core) to get numerical results of heat transfer and pressure drop coefficients, which are impacted mostly by the entrance of air ducts. The numerical calculations considered three-dimensional, steady-state, incompressible and turbulent flow; and were based on the Finite Volume methodology. The turbulent flow computations were carried out with procedures based on RANS equations by selecting k-omega SST (Shear-Stress Transport) as turbulence model. Grid quality metrics were monitored and the uncertainties due to discretization errors were evaluated by means of a grid independence study and application of an uncertainty estimation procedure based on Richardson extrapolation. The validation of numerical method developed by the present work (specifically to simulate the flow dynamics behavior and to obtain numerically the pressure drop coefficient of the airflow to enter and pass through the Stator Core Air Duct in a hydrogenerator) is performed by comparing the numerical results to experimental data published by Wustmann (2005). The reference experimental data were obtained by a model test. The comparison between numerical and experimental results shows that the difference of pressure drop for Reynolds numbers higher than 5000 is 2% at maximum, while for lower Reynolds numbers, the difference increases significantly and reaches 10%. It is presented that the most reasonable hypothesis for higher discrepancy at lower Reynolds numbers can be assigned to the experiment\'s non-steady-state condition. It is to conclude that the proposed numerical method is validated for the upper region of the analyzed range. Additionally to the model test validation, field measurements were executed in order to confirm numerical results. Measurements of pressure drop in the stator core of a real hydrogenerator were a challenge. Nevertheless, despite all the difficulties and considerable high field measuring uncertainties, trend curves behavior are similar to numerical results. Finally, series of numerical calculation, varying geometrical parameters of the air-duct inlet design and operational data, were done in order to obtain pressure drop coefficients trend curves to be directly applied to analytical calculation routines of whole hydrogenerator ventilation systems. Parallel to it, thermal numerical calculation was executed in the prototype simulation in order to define the convective heat transfer coefficient.O objetivo do presente trabalho é determinar os coeficientes de perda de carga e transferência de calor, normalmente aplicados nos cálculos analíticos de design térmico de hidrogeradores, obtido pela aplicação de cálculo numérico (Computacional Fluid Dynamics - CFD) e validado por resultados experimentais e medições de campo. O objeto de estudo é limitado à região mais importante do sistema de ventilação (os dutos de ar de arrefecimento do núcleo do estator) para obter resultados numéricos dos coeficientes de transferência de calor e de perda de carga, que são impactados principalmente pela entrada de dutos de ar. Os cálculos numéricos consideraram escoamentos tridimensionais, em regime permanente, incompressíveis e turbulentos; e foram baseados no método dos volumes finitos. Os cálculos de escoamento turbulento foram realizados com procedimentos baseados em equações médias (RANS), utilizando o modelo k-omega SST (Shear-Stress Transport) como modelo de turbulência. Métricas de qualidade de malha foram monitoradas e as incertezas devido à erros de discretização foram avaliadas por meio de um estudo de independência de malha e aplicação de um procedimento de estimativa de incertezas com base na extrapolação de Richardson. A validação do método numérico desenvolvido pelo presente trabalho (especificamente para simular o comportamento dinâmico do escoamento e obter numericamente o coeficiente de perda de carga do escoamento ao entrar no duto de ar e atravessar o núcleo do estator de um hidrogerador) é realizada comparando os resultados numéricos com dados experimentais publicados por Wustmann (2005). Os dados experimentais foram obtidos como referência por um teste de modelo. A comparação entre os resultados numéricos e experimentais mostra que a diferença da perda de carga para números de Reynolds mais elevados do que 5000 é no máximo de 2%, enquanto que para números de Reynolds inferiores, a diferença aumenta significativamente e atinge 10%. A hipótese mais razoável para a maior discrepância para número de Reynolds menores é a possível influência de instabilidades do escoamento no experimento, fazendo com que o regime seja não-permanente. Conclui-se que o método numérico proposto é validado para a região superior do intervalo analisado. Além da validação pelo ensaio de modelo, medições de campo foram executadas, a fim de confirmar os resultados numéricos. As medições de perda de carga no núcleo do estator de um hidrogerador real era um desafio. No entanto, apesar de todas as dificuldades e consideráveis incertezas da medição campo, o comportamento das curvas de tendência ficou alinhado com resultados numéricos. Finalmente, uma série de cálculos numéricos, variando parâmetros geométricos do design da entrada do duto de ar e dados operacionais, foram executados a fim de se obter curvas de tendência para coeficientes de perda de carga (resultados deste trabalho) a serem aplicadas diretamente à rotinas de cálculos analíticos de sistemas completos de ventilação de hidrogeradores. Paralelamente à isso, o cálculo térmico numérico foi executado na simulação do protótipo, a fim de se definir o coeficiente de transferência de calor por convecção.
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Morris, Seth Henderson. "Quasi-Transient Calculation of Surface Temperatures on a Reusable Booster System with High Angles of Attack." University of Dayton / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1324573899.
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Regmi, Hem Kanta. "A Real-Time Computational Decision Support System for Compounded Sterile Preparations using Image Processing and Artificial Neural Networks." University of Toledo / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1469113622.
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Löfås, Peter. "Advanced Traffic Service." Thesis, Linköping University, Department of Computer and Information Science, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-374.
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More and more travellers use navigation-aid software to find the way while driving. Most of todays systems use static maps with little or no information at all about currently yeilding roads conditions and disturbances in the network. It is desirable for such services
in the future to include information about road works, accidents, surface conditions and other types of events that affects what route is currently the best.
It is also desirable to notify users about changes in the prerequisites of the chosen route after they have started their trip.
This thesis investigates methods to include dynamic traffic information in route calculations and notifying users when the characteristics change for their chosen route.
The thesis utilizes dynamic traffic information from The Swedish Road Agencys (Vägverket) central database for traffic information, TRISS and calculates affected clients with help of positioning through the GSM network.
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López, Claudio David. "Shortening time-series power flow simulations for cost-benefit analysis of LV network operation with PV feed-in." Thesis, Uppsala universitet, Elektricitetslära, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-242099.
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Time-series power flow simulations are consecutive power flow calculations on each time step of a set of load and generation profiles that represent the time horizon under which a network needs to be analyzed. These simulations are one of the fundamental tools to carry out cost-benefit analyses of grid planing and operation strategies in the presence of distributed energy resources, unfortunately, their execution time is quite substantial. In the specific case of cost-benefit analyses the execution time of time-series power flow simulations can easily become excessive, as typical time horizons are in the order of a year and different scenarios need to be compared, which results in time-series simulations that require a rather large number of individual power flow calculations. It is often the case that only a set of aggregated simulation outputs is required for assessing grid operation costs, examples of which are total network losses, power exchange through MV/LV substation transformers, and total power provision from PV generators. Exploring alternatives to running time-series power flow simulations with complete input data that can produce approximations of the required results with a level of accuracy that is suitable for cost-benefit analyses but that require less time to compute can thus be beneficial. This thesis explores and compares different methods for shortening time-series power flow simulations based on reducing the amount of input data and thus the required number of individual power flow calculations, and focuses its attention on two of them: one consists in reducing the time resolution of the input profiles through downsampling while the other consists in finding similar time steps in the input profiles through vector quantization and simulating them only once. The results show that considerable execution time reductions and sufficiently accurate results can be obtained with both methods, but vector quantization requires much less data to produce the same level of accuracy as downsampling. Vector quantization delivers a far superior trade-off between data reduction, time savings, and accuracy when the simulations consider voltage control or when more than one simulation with the same input data is required, as in such cases the data reduction process can be carried out only once. One disadvantage of this method is that it does not reproduce peak values in the result profiles with accuracy, which is due to the way downsampling disregards certain time steps in the input profiles and to the averaging effect vector quantization has on the them. This disadvantage makes the simulations shortened through these methods less precise, for example, for detecting voltage violations.
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Duvenage, Eugene. "miRNAMatcher: High throughput miRNA discovery using regular expressions obtained via a genetic algorithm." Thesis, University of the Western Cape, 2008. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_5752_1266536340.
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In summary there currently exist techniques to discover miRNA however both require many calculations to be performed during the identification limiting their use at a genomic level. Machine learning techniques are currently providing the best results by combining a number of calculated and statistically derived features to identify miRNA candidates, however almost all of these still include computationally intensive secondary-structure calculations. It is the aim of this project to produce a miRNA identification process that minimises and simplifies the number of computational elements required during the identification process.
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Humayun, Mohammed Adel. "A hybrid approach for turbulent flow calculations." Thesis, University of Salford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272623.
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Crossley, Peter Simon. "On spectral methods for shock wave calculations." Thesis, Manchester Metropolitan University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361577.
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Lindstens, Robin. "Computational fluid dynamics calculations of a spillway’s energy dissipation." Thesis, Uppsala universitet, Institutionen för fysik och astronomi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-417950.
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To make sure that a dam is safe it is important to have good knowledge about the energy dissipation in the spillway. Physical hydraulic model tests are reliable when investigating how the water flow behaves on its way through the spillway. The problem with physical model testing is that it is both expensive and time consuming, therefore computational fluid dynamics, CFD, is a more feasible option. This projects focuses on a spillway located in Sweden that Vattenfall R&D built a physical model of to simulate the water discharge and evaluate the energy dissipation in order to rebuild the actual spillway. The main purpose of this project is to evaluate if the physical hydraulic test results can be reproduced by using CFD, and obtain detailed results about the flow that could not be obtained by physical testing. There are several steps that need to be completed to create a CFD-model. The first step is to create a geometry, then the geometry needs to be meshed. After the meshing the boundary conditions need to be set and the different models, multiphase model and the viscous model, need to be defined. Next step is to set the operating conditions and decide which solution method that will be used. Then the simulation can be run and the results can get extracted. In this project two CFD simulations were performed. The first simulation was to be compared with the physical hydraulic model test results and the second CFD simulation was of the rebuilt spillway. The results proved that the physical model test results could be recreated by using CFD. It also gave a better understanding of how the energy dissipation was in the spillway and indicates that the reconstruction of the actual spillway was successful since the new spillway both had a higher water discharge capacity and better energy dissipation.
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Saffar, Shamshirgar Davood. "Fast methods for electrostatic calculations in molecular dynamics simulations." Doctoral thesis, KTH, Numerisk analys, NA, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-219775.
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This thesis deals with fast and efficient methods for electrostatic calculations with application in molecular dynamics simulations. The electrostatic calculations are often the most expensive part of MD simulations of charged particles. Therefore, fast and efficient algorithms are required to accelerate these calculations. In this thesis, two types of methods have been considered: FFT-based methods and fast multipole methods (FMM). The major part of this thesis deals with fast N.log(N) and spectrally accurate methods for accelerating the computation of pairwise interactions with arbitrary periodicity. These methods are based on the Ewald decomposition and have been previously introduced for triply and doubly periodic problems under the name of Spectral Ewald (SE) method. We extend the method for problems with singly periodic boundary conditions, in which one of three dimensions is periodic. By introducing an adaptive fast Fourier transform, we reduce the cost of upsampling in the non periodic directions and show that the total cost of computation is comparable with the triply periodic counterpart. Using an FFT-based technique for solving free-space harmonic problems, we are able to unify the treatment of zero and nonzero Fourier modes for the doubly and singly periodic problems. Applying the same technique, we extend the SE method for cases with free-space boundary conditions, i.e. without any periodicity. This thesis is also concerned with the fast multipole method (FMM) for electrostatic calculations. The FMM is very efficient for parallel processing but it introduces irregularities in the electrostatic potential and force, which can cause an energy drift in MD simulations. In this part of the thesis we introduce a regularized version of the FMM, useful for MD simulations, which approximately conserves energy over a long time period and even for low accuracy requirements. The method introduces a smooth transition over the boundary of boxes in the FMM tree and therefore it removes the discontinuity at the error level inherent in the FMM.QC 20171213
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Greene, William H. "Computational aspects of sensitivity calculations in linear transient structural analysis." Diss., Virginia Polytechnic Institute and State University, 1989. http://hdl.handle.net/10919/54180.
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A study has been performed focusing on the calculation of sensitivities of displacements, velocities, accelerations, and stresses in linear, structural, transient response problems. One significant goal of the study was to develop and evaluate sensitivity calculation techniques suitable for large-order finite element analyses. Accordingly, approximation vectors such as vibration mode shapes are used to reduce the dimensionality of the finite element model. Much of the research focused on the accuracy of both response quantities and sensitivities as a function of number of vectors used.
Two types of sensitivity calculation techniques were developed and evaluated. The first type of technique is an overall finite difference method where the analysis is repeated for perturbed designs. The second type of technique is termed semianalytical because it involves direct, analytical differentiation of the equations of motion with finite difference approximation of the coefficient matrices. To be computationally practical in large-order problems, the overall finite difference methods must use the approximation vectors from the original design in the analyses of the perturbed models. In several cases this fixed mode approach resulted in very poor approximations of the stress sensitivities. Almost all of the original modes were required for an accurate sensitivity and for small numbers of modes, the accuracy was extremely poor. To overcome this poor accuracy, two semi-analytical techniques were developed. The first technique accounts for the change in eigenvectors through approximate eigenvector derivatives. The second technique applies the mode acceleration method of transient analysis to the sensitivity calculations. Both result in accurate values of the stress sensitivities with a small number of modes. In both techniques the computational cost is much less than would result if the vibration modes were recalculated and then used in an overall finite difference method.Ph. D.
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Ross, Gregory A. "Improving rapid affinity calculations for drug-protein interactions." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:62ccfb5e-10f1-40ec-9a2b-936277944d87.
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The rationalisation of drug potency using three-dimensional structures of protein-ligand complexes is a central paradigm in medicinal research. For over two decades, a major goal has been to find the rules that accurately relate the structure of any protein-ligand complex to its affinity. Addressing this problem is of great concern to the pharmaceutical industry, which uses virtual screens to computationally assay up to many millions of compounds against a protein target. A fast and trustworthy affinity estimator could potentially streamline the drug discovery process, reducing reliance on expensive wet lab experiments, speeding up the discovery of new hits and aiding lead optimization. Water plays a critical role in drug-protein interactions. To address the often ambiguous nature of water in binding sites, a water placement method was developed and found to be in good agreement with X-ray crystallography, neutron diffraction data and molecular dynamics simulations. The method is fast and has facilitated a large scale study of the statistics of water in ligand binding sites, as well as the creation of models pertaining to water binding free energies and displacement propensities, which are of particular interest to medicinal chemistry. Structure-based scoring functions employing the explicit water models were developed. Surprisingly, these attempts were no more accurate than the current state of the art, and the models suffered from the same inadequacies which have plagued all previous scoring functions. This suggests a unifying cause behind scoring function inaccuracy. Accordingly, mathematical analyses on the fundamental uncertainties in structure-based modelling were conducted. Using statistical learning theory and information theory, the existence of inherent errors in empirical scoring functions was proven. Among other results, it was found that even the very best generalised structure-based model is significantly limited in its accuracy, and protein-specific models are always likely to be better. The theoretical framework developed herein hints at modelling strategies that operate at the leading edge of achievable accuracy.
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Rau, Lisa F. "A computational approach to meta-knowledge : calculating breadth and salience." Thesis, University of Exeter, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332589.
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Panel, Nicolas. "Étude computationnelle du domaine PDZ de Tiam1." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX062/document.
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Les interactions protéine-protéine sont souvent contrôlées par de petits domaines protéiques qui régulent les chemins de signalisation au sein des cellules eucaryotes. Les domaines PDZ sont parmi les domaines les plus répandus et les plus étudiés. Ils reconnaissent spécifiquement les 4 à 10 acides aminés C-terminaux de leurs partenaires. Tiam1 est un facteur d'échange de GTP de la protéine Rac1 qui contrôle la migration et la prolifération cellulaire et dont le domaine PDZ lie les protéines Syndecan-1 (Sdc1), Caspr4 et Neurexine. Des petits peptides ou des molécules peptidomimétiques peuvent potentiellement inhiber ou moduler son activité et être utilisés à des fins thérapeutiques. Nous avons appliqué des approches de dessin computationnel de protéine (CPD) et de calcul d'énergie libre par simulations dynamique moléculaire (DM) pour comprendre et modifier sa spécificité. Le CPD utilise un modèle structural et une fonction d'énergie pour explorer l'espace des séquences et des structures et identifier des variants protéiques ou peptidiques stables et fonctionnels. Nous avons utilisé le programme de CPD Proteus, développé au laboratoire, pour redessiner entièrement le domaine PDZ de Tiam1. Les séquences générées sont similaires à celles des domaines PDZ naturels, avec des scores de similarité et de reconnaissance de pli comparables au programme Rosetta, un outil de CPD très utilisé. Des séquences contenant environ 60 positions mutées sur 90, ont été testées par simulations de DM et des mesures biophysiques. Quatre des cinq séquences testées expérimentalement (par nos collaborateurs) montrent un dépliement réversible autour de 50°C. Proteus a également déterminer correctement la spécificité de la liaison de quelques variants protéiques et peptidiques. Pour étudier plus finement la spécificité, nous avons paramétré un modèle d'énergie libre semi-empirique de Poisson-Boltzmann ayant la forme d'une énergie linéaire d'interaction, ou PB/LIE, appliqué à des conformations issues de simulations de DM en solvant explicite de complexes PDZ:peptide. Avec trois paramètres ajustables, le modèle reproduit correctement les affinités expérimentales de 41 variants, avec une erreur moyenne absolue de 0,4~kcal/mol, et donne des prédictions pour 10 nouveaux variants. Le modèle PB/LIE a ensuite comparé à la méthode non-empirique de calcul d'énergie libre par simulations alchimiques, qui n'a pas de paramètre ajustable et qui prédit correctement l'affinité de 12 complexes Tiam1:peptide. Ces outils et les résultats obtenus devraient nous permettre d'identifier des peptides inhibiteurs et auront d'importantes retombées pour l'ingénierie des interactions PDZ:peptideSmall protein domains often direct protein-protein interactions and regulate eukaryotic signalling pathways. PDZ domains are among the most widespread and best-studied. They specifically recognize the 4-10 C-terminal amino acids of target proteins. Tiam1 is a Rac GTP exchange factor that helps control cellmigration and proliferation and whose PDZ domain binds the proteins syndecan-1 (Sdc1), Caspr4, and Neurexin. Short peptides and peptidomimetics can potentially inhibit or modulate its action and act as bioreagents or therapeutics. We used computational protein design (CPD) and molecular dynamics (MD) free energy simulations to understand and engineer its peptide specificity. CPD uses a structural model and an energy function to explore the space of sequences and structures and identify stable and functional protein or peptide variants. We used our in-house Proteus CPD package to completely redesign the Tiam1 PDZ domain. The designed sequences were similar to natural PDZ domains, with similarity and fold recognition scores comarable to the widely-used Rosetta CPD package. Selected sequences, containing around 60 mutated positions out of 90, were tested by microsecond MD simulations and biophysical experiments. Four of five sequences tested experimentally (by our collaborators) displayed reversible unfolding around 50°C. Proteus also accurately scored the binding specificity of several protein and peptide variants. As a more refined model for specificity, we parameterized a semi-empirical free energy model of the Poisson-Boltzmann Linear Interaction Energy or PB/LIE form, which scores conformations extracted from explicit solvent MD simulations of PDZ:peptide complexes. With three adjustable parameters, the model accurately reproduced the experimental binding affinities of 41 variants, with a mean unsigned error of just 0.4 kcal/mol, andgave predictions for 10 new variants. The PB/LIE model was tested further by comparing to non-empirical, alchemical, MD free energy simulations, which have no adjustable parameters and were found to give chemical accuracy for 12 Tiam1:peptide complexes. The tools and insights obtained should help discover new tight binding peptides or peptidomimetics and have broad implications for engineering PDZ:peptide interactions
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Shafer, Lawrence E. "Data Driven Calculations Histories to Minimize IEEE-755 Floating-point Computational Error." NSUWorks, 2004. http://nsuworks.nova.edu/gscis_etd/830.
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The widely implemented and used IEEE-754 Floating-point specification defines a method by which floating-point values may be represented in fixed-width storage. This fixed-width storage does not allow the exact value of all rational values to be stored. While this is an accepted limitation of using the IEEE-754 specification, this problem is compounded when non-exact values are used to compute other values. Attempts to manage this problem have been limited to software implementations that require special programming at the source code level. While this approach works, the problem coder must be aware of the software and explicitly write high-level code specifically referencing it. The entirety of a calculation is not available to the special software so optimum results cannot always be obtained when the range of operand values is large. This dissertation proposes and implements an architecture that uses integer algorithms to minimize precision loss in complex floating-point calculations. This is done using runtime calculation operand values at a simulated hardware level. These calculations are coded in a high-level language such that the coder is not knowledgeable about the details of how the calculation is performed.
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Hogg, Simon I. "Second-moment-closure calculations of strongly-swirling confined flows with and without density variations." Thesis, University of Manchester, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328638.
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Becat-Mateu, Damien. "Integration of gamma computations in a calculation chain combining APOLLO2 and CRONOS2." Thesis, KTH, Fysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-250321.
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Eklund, Robert. "Computational Analysis of Carbohydrates : Dynamical Properties and Interactions." Doctoral thesis, Stockholm : Department of Organic Chemistry, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-538.
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Villa, Francesco. "Computer simulations to engineer PDZ-peptide recognition." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX076/document.
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Les interactions protéine-protéine (IPPs) médient la signalisation cellulaire. Leur ingénierie peut fournir des informations et conduire au développement de molécules thérapeutiques. Les domaines PDZ sont des médiateurs importants de IPPs. Elles lient les 4--10 résidus C-terminaux de protéines cibles. Elles lient aussi les peptides correspondants, qui peuvent servir de systèmes modèles ou d'inhibiteurs. Nous avons développé deux approches computationnelles et les avons appliquées au domaine PDZ de la protéine Tiam1, un facteur d'échange pour la protéine Rac, impliqué dans la protrusion neuronale. Sa cible est la protéine Syndecan1. Des affinités expérimentales sont connues pour le peptide C-terminal, noté Sdc1, et plusieurs mutants; elles ont servi pour tester les calculs. Nous avons d'abord développé une méthode de dessin computationnel haut débit. Une simulation Monte Carlo est faite où les chaines latérales de la protéine et du peptide peuvent changer de conformères et certaines positions peuvent muter. Le solvant est implicite. Le paysage énergétique est aplati par la méthode adaptative de Wang-Landau, de sorte qu'un vaste ensemble de variantes est échantillonné. Effectuant des simulations distinctes du complexe et du peptide seul nous avons obtenu les énergies libres relatives d'association de 75,000 variantes en heure CPU sur une machine de bureau. Les valeurs sont compatibles avec les quelques données expérimentales disponibles. Ensuite, nous avons développé une approche beaucoup plus détaillée et réaliste. Soluté et solvant sont décrits par un champ de force atomique, qui représente explicitement la polarisation électronique: le champ de force Drude de Charmm. La polarisabilité peut être importante car les résidus de l'interface PDZ:peptide passent, lors de l'association, d'un environnement riche en solvant à un autre pauvre en solvant. Nous avons fait des simulations alchimiques d'énergie libre pour comparer quatre variantes du peptide qui diffèrent par une ou deux chaines latérales ioniques. Les résultats sont en bon accord avec l'expérience. Les champs de force additifs Charmm et Amber, qui représentent la polarisabilité implicitement, donnent un moins bon accord. Ces calculs sont le premier exemple de simulations alchimiques d'énergies libre d'association relatives protéine: ligand avec un champ de force polarisable. Enfin, pour une modélisation future de peptides phosphorylés, nous avons étendu le champ de force Drude pour inclure le méthyl phosphate et la phospho tyrosine. Il en résulte un excellent accord avec les affinités expérimentales phosphate: magnésiumProtein-protein interactions (PPIs) regulate complex signaling networks in eukaryotic cells. Many binding events between several protein domains transfer information through communication pathways. Disrupting or altering the equilibrium between PPIs plays an important role inseveral diseases and the inibition of targeted PPIs is a recognized strategy for computational drug design. In the present thesis we focused on PDZ domains, which are among the most widespread signaling domains. PDZs recognize the 4-10 C-terminal amino acids of their target proteins as well as the corresponding peptides in isolation. We studied PDZ:peptide binding for the Tiam1 protein, which is a Rac GTP exchange factor involved in neuronal protrusion and axon guidance. Tiam1 activity modulates signaling for cell proliferation and migration, whose dysregulation increases growth of metastatic cancers. Its natural binder peptide is Syndecan1 (Sdc1), composed of 8 amino acids. Its last 5 Cter residues drive interactions in the binding pocket. Experimental affinities for several mutants of Sdc1 and in the protein domain constitute a complete dataset to study many ionic interactions with molecular simulations. These calculations are still challenging, despite the dramatic improvement of biomolecular modelling in the 1990's and 2000's. Upon binding, residues are transferred from a solvent-exposed environment to a solvent-poor one. This is expected to change the electron distribution within residues and nearby solvent molecules. Comparing ligands that differ by one or more ionic side-chain mutations, more sophisticated force fields where electronic polarizability is treated explicitly may be required. We developed and tested both Computational Protein Design (CPD) models and more precise free energy calculation methods based on polarizable molecular dynamics. We developed a general, high-througtput CPD protocol to optimize protein:peptide binding. The model has been implemented in on our in-house CPD package Proteus ( Simonson et al, 2014) and has been tested computing relative binding affinities for many variants of the Tiam1:Sdc1 complex. Monte Carlo sampling of equilibrium distributions of protein sequences is performed using an adaptive bias potential which flattens the energy landscape in sequence space and allows to estimate binding affinities for thousands of protein variants in limited CPU time (~1hour). We also improved our CPD implicit solvent model, implementing a more realistic description of the solute-solvent dielectric boundary. The new method, called Fluctuating Dielectric Boundary (FDB) showed a systematic improvement in the prediction of acid:base constants of several proteins. Promising results were also obtained for the complete sequence redesign of three PDZ domains. In the second part of this work we studied Tiam1:peptide affinities with more sophisticated models, based on free energy simulations with the Drude Polarizable Force field (DrudeFF). We first computed relative binding free energies for charge mutations in the Tiam1:Sdc1 complex, obtaining a clear improvement respect to equivalent calculations performed using two additive force fields. We applied the well-enstablished Dual Topology Approach: to our knowledge, this was the first example of such a calculation for a protein:peptide complex with uses the DrudeFF. Then we went on, developing the Drude polarizable models for methyl phosphate (MP) and phospho tyrosine (pTyr). We were interested in the change in binding affinity associated with phosphorylation of a Tyrosine residue of Sdc1, but Drude pTyr parameters were not yet developed. We tested our new phosphate parameters studying standard binding free energies between MP and magnesium (Mg2+) in water solution. Results showed a good agreement with experiment, improving previous calculations performed using additive force field
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Vazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.
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This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).
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Shamsudin, Khan Yasmin. "Computational methods for calculating binding free energies of ligands in COX-1." Licentiate thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-226069.
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Kendall, Treavor Allen. "Exploring Siderophore-Mineral Interaction Using Force Microscopy and Computational Chemistry." Diss., Virginia Tech, 2003. http://hdl.handle.net/10919/26961.
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The forces of interaction were measured between the siderophore azotobactin and the minerals goethite (FeOOH) and diaspore (AlOOH) in solution using force microscopy. Azotobactin was covalently linked to a hydrazide terminated atomic force microscope tip using a standard protein coupling technique. Upon contact with each mineral surface, the adhesion force between azotobactin and goethite was two to three times the value observed for the isostructural Al-equivalent diaspore. The affinity for the solid iron oxide surface reflected in the force measurements correlates with the specificity of azotobactin for aqueous ferric iron. Further, the adhesion force between azotobactin and goethite significantly decreases when small amounts of soluble iron are added to the system suggesting a significant specific interaction between the azotobactin and the mineral surface. Changes in the force signature with pH and ionic strength were fairly predictable when considering mineral solubility, the charge character of the mineral surfaces, the molecular structure of azotobactin, and the intervening solution.
Molecular and quantum mechanical calculations which were completed to further investigate the interaction between azotobactin and iron/aluminum oxide surfaces, and to more fully understand the force measurements, also showed an increased force affinity for Fe over Al. Ab initio calculations on siderophore fragment analogs suggest the iron affinity can be attributed to increased electron density associated with the Fe-O bond compared to the Al-O bond; an observation that correlates with ironâ s larger electronegativity compared to aluminum. Attachment of the ligand to each surface was directed by steric forces within the molecule and coulombic interactions between the siderophore oxygens and the metals in the mineral. Chelating ligand pairs coordinated with neighboring metal atoms in a bidentate, binuclear geometry. Upon simulated retraction of azotobactin from each surface, the Fe-O(siderophore) bonds persisted into a higher force regime than Al-O(siderophore) bonds, and surface metals were removed from both minerals. Extrapolation of the model to more realistic hydrated conditions using a PCM model in the quantum mechanical calculations and water clusters in the molecular mechanical model demonstrated that the presence of water energetically favors and enhances metal extraction, making this a real possibility in a natural system.Ph. D.
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Zheng, Lixin. "Properties of Liquid Water and Solvated Ions Based on First Principles Calculations." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/527565.
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PhysicsPh.D.
Water is of essential importance for life on earth, yet the physics concerning its various anomalous properties has not been fully illuminated. This thesis is dedicated to the understanding of liquid water from aspects of microscopic structures, dynamics, electronic structures, X-ray absorption spectra, and proton transfer mechanism. This thesis use the computational simulation techniques including density functional theory (DFT), ab initio molecular dynamics (AIMD), and theoretical models for X-ray absorption spectra (XAS) to investigate the dynamics and electronic structures of liquid water system. The topics investigated in this thesis include a comprehensive evaluation on the simulation of liquid water using the newly developed SCAN meta-GGA functional, a systematic modeling of the liquid-water XAS using advanced ab initio approaches, and an explanation for a long-puzzling question that why hydronium diffuses faster than hydroxide in liquid water. Overall, significant contributions have been made to the understanding of liquid water and ionic solutions in the microscopic level through the aid of ab initio computational modeling.
Temple University--Theses
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Heggarty, Jonathan W. "Parallel R-matrix computation." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287468.
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Kodikara, Mahesh Sanjaya. "Computational Study of Structural and Optical Properties of Metal Alkynyl Complexes." Phd thesis, Canberra, ACT : The Australian National University, 2017. http://hdl.handle.net/1885/143293.
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The interaction of light with a nonlinear optical (NLO)
material gives rise to new optical fields with altered properties
(e.g. phase, frequency, amplitude, polarization, path, etc.),
which are of utmost importance for photonic applications. The
search for new efficient NLO materials for applications has thus
been accelerated. In particular, interest in the NLO properties
of organometallic systems has undergone enormous growth in the
past decade. This thesis consists of a compilation of several
papers relating to the experimental and density functional theory
(DFT) studies of the nonlinear optical properties of metal
alkynyl complexes. Paper 1 includes a brief introduction to
nonlinear optical phenomena, in particular to the second-order
NLO effects, and the popular experimental and quantum chemical
methods for the determination of molecular first
hyperpolarizability. It also includes a comprehensive review of
previous semi empirical and DFT NLO calculations relating to
organometallic complexes. Paper 2 deals with the benchmarking of
DFT methods for first hyperpolarizabilities and excitation
energies of metal alkynyls against the relevant experimental
data. Papers 3-9 are combined experimental and computational
(DFT) studies of dipolar (paper 3-8) and octupolar (paper 9)
metal alkynyl complexes. The contribution from the calculations
to each paper is as follows. In paper 3, linear optical and
quadratic nonlinear optical properties of alkynyl complexes with
different ligated metal centres (Ru, Ni, and Au) and with
different bridges (phenylene, naphthalenylene, and
anthracenylene) are calculated with DFT and time dependent DFT
(TD-DFT). In paper 4, the linear optical and quadratic nonlinear
optical properties of ruthenium alkynyl complexes with
oligo(phenylenevinylene) bridges were calculated using DFT and
the results compared with the experimental data. In paper 5, the
experimentally determined linear optical properties and first
hyperpolarizabilities of some ruthenium alkynyl complexes with
yne/ene/azo inter-ring linkers are rationalized by DFT/TD-DFT
calculations. In paper 6, the structural, linear optical, and
nonlinear optical properties of ruthenium alkynyl complexes with
P–P (= dppf, dppb, and dppe) and N–N
(4,4’-di-tert-butyl-2,2’-bipyridine) donor co-ligands were
rationalized from DFT calculations. Paper 7 consists of TD-DFT
calculations undertaken on a series of bis(alkynyl) Ru complexes
to rationalize the experimental linear optical data. In paper 8,
the mechanism of two-dimensional NLO character in Y-shaped
ruthenium alkynyl complexes is studied with the use of DFT/TD-DFT
calculations. In paper 9, computational studies were undertaken
to assign the key optical transitions for some octupolar
compounds bearing (N-heterocyclic carbene) gold or diphenylamino
substituents at the periphery.
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Hoogkamp, Eric. "Calculations of Light-Matter Interactions in Dielectric Media Using Microscopic Particle-in-Cell Technique." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35530.
Full textAbstract:
The interaction between light and matter is usually modeled by approximating the material under study as a continuum. The magnitude of the material's polarization in the presence of an electric field is dependent on the atomic response via the well-known Lorentz-Lorentz relation. These continuous medium models can be used to see many light-matter effects including non-linear interactions.The goal of this thesis is to adapt and use novel computational methods to explore the microscopic origins of non-linear optical effects. The Microscopic Particle-in-Cell (MicPIC) technique, initially developed to model the laser-driven dynamics of strongly-coupled plasmas, is extended to study the non-linear scattering of light by a collection of dipoles in the atomic limit. In this thesis, we find that in one-dimensional chains of individual scatterers there are apparent boundary effects and the generation of even harmonics that do not appear in continuous media calculations.These finite structures of dipoles also exhibit a lower average response from each at odd harmonic frequencies of the driving light frequency.These results are in contradiction with the commonly used Lorentz-Lorenz relation, derived for a dipole in a 3D material with infinite volume, and suggest that MicPIC is more appropriate for calculations of nanostructures than models using the Lorentz-Lorenz relation.
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Mahmoud, S. A. "Motion detection and velocity computation of moving objects in time-varying image sequences : Application of the exponential area transform in computation of presence and velocity of objects of different sizes and occurences." Thesis, University of Bradford, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379903.
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Reid, Jolene Patricia. "Development and application of computational methods for the prediction of chiral phosphoric acid catalyst performance." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/269024.
Full textAbstract:
Chiral phosphoric acids are bifunctional catalysts that have the ability to activate electrophiles and nucleophiles through hydrogen bonding, and they have been successful in catalysing highly enantioselective additions of a wide range of nucleophiles to imines. In most literature reports it is not frequently revealed how these catalysts impart enantioselectivity. Thus, the vast majority of time required for reaction development is expended on the optimisation of the catalyst features. The research described here explores the ability of relating computational derived catalyst parameters to enantioselectivity as a means to assess the catalyst features important for enantioinduction. The proposed features are evaluated computationally and summarised into simple qualitative models to understand and predict outcomes of similar reactions. In Chapter 1, I provide an overview of the progress and challenges in the development of chiral phosphoric acid mediated reactions. I highlight leading computational studies that have enabled a greater understanding of how the catalyst imparts reactivity and selectivity. In general, the studies focus on the most effective catalyst and do not do a detailed investigation into the effects of changing the substituents at the 3,3’ positions. Implicating steric effects from reasonably large groups as a key component in imparting enantioselectivity. However, it is clear that they have a more subtle effect. A large group is required but if it is too large poor or unusual results are obtained, making the correct choice of reaction conditions challenging. In Chapter 2, I develop a quantitative assessment of the substituents at the 3,3’ positions. I show in Chapters 3 and 4 that I can use rotation barriers in combination with a novel steric parameter, AREA(θ), to correlate enantioselectivity. By exploiting this finding, the catalyst features important for enantioselectivity can be identified, and this is validated by QM/MM hybrid calculations. Summarising these detailed calculations into a single qualitative model, guides optimal catalyst choice for all seventy-seven literature reactions reporting over 1000 transformations. These mechanistic studies have guided the design of a new catalyst with increased versatility, which is discussed in Chapter 5. Chapter 6 details my study into the effect of the hydroxyl group on the mechanism of transfer hydrogenation of imines derived from ortho-hydroxyacetophenone. I show, using detailed DFT and ONIOM calculations, that transition states of these reactions involve hydrogen bonding from both the hydroxyl group on the imine and the nucleophile’s proton to the phosphate catalyst. In Chapter 7, computational analysis is used to provide insight into the origins of enantioselectivity in chiral phosphoric acid catalysed Friedel-Crafts and Mannich reactions proceeding through monoactivation mechanisms. The final chapter contains an in-depth look into the stereoelectronic effects altering enantioselectivity in the silver-phosphate mediated spirocyclisation reaction involving aromatic ynones. In this study I show that enantioselectivity is governed by the non-covalent interactions between the aromatic group of the ynone and the 3,3’ substituent. I was able to propose synthetic modifications to the substrate used in this reaction, resulting in an improvement in enantioselectivity.
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Ruiz-Serrano, Alvaro. "Computational methods for density functional theory calculations on insulators and metals based on localised orbitals." Thesis, University of Southampton, 2013. https://eprints.soton.ac.uk/360145/.
Full textAbstract:
Kahn-Sham density functional theory (OFT) calculations yield reliable accuracy in a wide variety of molecules and materials. The advent of linear-scaling OFT methods, based on locality of the electronic matter, has enabled calculations on systems with tens of thousands of atoms. Localisation constraints are imposed by expanding the Kahn-Sham states in terms of a set of atom-centred, spherically-localised functions. Chemical accuracy is then achieved via a self-consistent optimisation using a high-resolution basis set. This formalism reduces the size of, and brings predictable sparsity patterns to, the matrices expressed in this representation, such as the Hamiltonian matrix. In this work, we used the ONETEP program for DFT calculations, which is based on the abovementioncd principles. The vision behind our research is to advance the method by developing new and robust algorithms to enable novel applications based on localised orbitals.
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Červinka, Martin. "Studie návrhu kalového čerpadla s vířivým kolem." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2011. http://www.nusl.cz/ntk/nusl-229991.
Full textAbstract:
Diploma thesis deals with problems of design a sludge pump with a vortex impeller. Clearly summarizes the basic information on hydrodynamic pumps with a significant focus on sludge pumps. It contains a design of a vortex impeller, which is supported by CFD (Computational Fluid Dynamic) calculation in software Fluent. The aim of the work is to design vortex impeller, which could replace the existing channel impeller while maintaining the operating parameters of the pump.
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South, Christopher James. "Quantum Chemistry Calculations of Energetic and Spectroscopic Properties of p- and f-Block Molecules." Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc862830/.
Full textAbstract:
Quantum chemical methods have been used to model a variety of p- and f-block chemical species to gain insight about their energetic and spectroscopic properties. As well, the studies have provided understanding about the utility of the quantum mechanical approaches employed for the third-row and lanthanide species. The multireference ab initio correlation consistent Composite Approach (MR-ccCA) was utilized to predict dissociation energies for main group third-row molecular species, achieving energies within 1 kcal mol-1 on average from those of experiment and providing the first demonstration of the utility of MR-ccCA for third-row species. Multireference perturbation theory was utilized to calculate the electronic states and dissociation energies of NdF2+, providing a good model of the Nd-F bond in NdF3 from an electronic standpoint. In further work, the states and energies of NdF+ were determined using an equation of motion coupled cluster approach and the similarities for both NdF2+ and NdF were noted. Finally, time-dependent density functional theory and the static exchange approximation for Hartree-Fock in conjunction with a fully relativistic framework were used to calculate the L3 ionization energies and electronic excitation spectra as a means of characterizing uranyl (UO22+) and the isoelectronic compounds NUO+ and UN2.
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Au, Edwin C. F. "A computational scheme for calculating refrigerant properties & heat transfer in boiling tube flow /." Title page, contents and abstract only, 1998. http://web4.library.adelaide.edu.au/theses/09ENS/09ensa888.pdf.
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Djayapertapa, Lesmana. "A computational method for coupled aerodynamic-structural calculations in unsteady transonic flow with active control study." Thesis, University of Bristol, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341506.
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