Дисертації з теми "Computational calculation"
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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/.
Повний текст джерелаBrown, 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.
Повний текст джерелаTang, 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.
Повний текст джерелаAlmlöf, 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.
Повний текст джерелаThe 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.
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.
Повний текст джерелаFey, Natalie. "Molecular modelling of ferrocenes and arylphosphines." Thesis, Keele University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368982.
Повний текст джерелаFosso-Tande, Jacob. "A Computational Chemistry Study of Spin Traps." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etd/2127.
Повний текст джерелаTang, 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.
Повний текст джерелаParasuram, 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.
Знайти повний текст джерела"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.
Castro, Aguilera Abril Carolina. "Computational study of nuclear magnetic shielding constants." Doctoral thesis, Universitat de Girona, 2017. http://hdl.handle.net/10803/565597.
Повний текст джерелаL’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
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.
Знайти повний текст джерелаPopov, 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.
Повний текст джерелаMachat, Mohamed. "Computational geometry for the determination of biomolecular structures." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066359/document.
Повний текст джерелаStructural 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
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.
Повний текст джерелаPh.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
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.
Повний текст джерелаThe 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.
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.
Повний текст джерелаGahm, 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.
Повний текст джерелаAltea, 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/.
Повний текст джерелаO 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.
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.
Повний текст джерелаRegmi, 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.
Повний текст джерелаLöfås, 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.
Повний текст джерелаMore 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.
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.
Повний текст джерелаDuvenage, 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.
Повний текст джерелаIn 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.
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.
Повний текст джерелаCrossley, 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.
Повний текст джерелаLindstens, 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.
Повний текст джерелаSaffar, 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.
Повний текст джерелаQC 20171213
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.
Повний текст джерелаPh. D.
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.
Повний текст джерелаRau, 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.
Повний текст джерелаPanel, Nicolas. "Étude computationnelle du domaine PDZ de Tiam1." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX062/document.
Повний текст джерелаSmall 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
Shafer, Lawrence E. "Data Driven Calculations Histories to Minimize IEEE-755 Floating-point Computational Error." NSUWorks, 2004. http://nsuworks.nova.edu/gscis_etd/830.
Повний текст джерелаHogg, 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.
Повний текст джерелаBecat-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.
Повний текст джерелаEklund, 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.
Повний текст джерелаVilla, Francesco. "Computer simulations to engineer PDZ-peptide recognition." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX076/document.
Повний текст джерелаProtein-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
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/.
Повний текст джерелаShamsudin, 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.
Повний текст джерелаKendall, Treavor Allen. "Exploring Siderophore-Mineral Interaction Using Force Microscopy and Computational Chemistry." Diss., Virginia Tech, 2003. http://hdl.handle.net/10919/26961.
Повний текст джерелаPh. D.
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.
Повний текст джерелаPh.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
Heggarty, Jonathan W. "Parallel R-matrix computation." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287468.
Повний текст джерелаKodikara, 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.
Повний текст джерелаHoogkamp, 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.
Повний текст джерелаMahmoud, 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.
Повний текст джерелаReid, 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.
Повний текст джерелаRuiz-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/.
Повний текст джерелаČervinka, 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.
Повний текст джерелаSouth, 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/.
Повний текст джерелаAu, 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.
Повний текст джерелаDjayapertapa, 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.
Повний текст джерела