Relevant bibliographies by topics / Ab initio prediction / Dissertations / Theses
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Dissertations / Theses on the topic 'Ab initio prediction'

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Published: 11 March 2023

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1

Thomas, Geraint Llewllyn. "Ab initio protein fold prediction." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436019.

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2

Meyer, Irmtraud Margret. "Mathematical methods for comparative Ab initio gene prediction." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619669.

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3

Djurdjević, Dušan. "Ab initio protein fold prediction using evolutionary algorithms." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/13660.

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A comprehensive study was undertaken for <i>ab initio </i>protein fold prediction using a fully atomistic protein model and a physicochemical potential. Twenty four EA designs where initially assessed on polyalanine, a prototypical α-helical polypeptide.  Design aspects varied include the encoding alphabet, crossover operator, replacement strategy and selection strategy. By undertaking a comprehensive parameter study, the best performing designs and associated control parameter values were identified for polyalanine. The scaling between the performance and polyalinine size was also identified
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4

Wang, Guisheng. "Ab initio prediction of the mechanical properties of alloys." Doctoral thesis, KTH, Tillämpad materialfysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-169511.

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At the time of the 50th anniversary of the Kohn-Sham method, ab initio calculations based on density functional theory have formed an accurate, efficient, and reliable method to work on the properties of engineering materials. In this thesis, we use the exact muffin-tin orbitals method combined with the coherent-potential approximation to study the mechanical properties of high-technology materials. The thesis includes two parts: a study of long-range chemical order effects and a study of alloying effects on the mechanical properties of alloys. In the first part, we concentrate on the impact o
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5

Kang, ShinYoung. "Ab initio prediction of thermodynamics in alkali metal-air batteries." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/89952.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Materials Science and Engineering, 2014.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 93-100).<br>Electric vehicles ("EVs") require high-energy-density batteries with reliable cyclability and rate capability. However, the current state-of-the-art Li-ion batteries only exhibit energy densities near ~150 Wh/kg, limiting the long-range driving of EVs with one charge and hindering their wide-scale commercial adoption.1-3 Recently, non-aqueous metal-O₂ batteries have drawn attention due to
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6

Mijajlovic, Milan. "Ab initio prediction of the conformation of solvated and adsorbed proteins." Thesis, University of Edinburgh, 2008. http://hdl.handle.net/1842/3173.

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Proteins are among the most important groups of biomolecules, with their biological functions ranging from structural elements to signal transducers between cells. Apart from their biological role, phenomena related to protein behaviour in solutions and at solid interfaces can find a broad range of engineering applications such as in biomedical implants, scaffolds for artificial tissues, bioseparations, biomineralization and biosensors. For both biological and engineering applications, the functionality of a protein is directly related to its three-dimensional structure (i.e. conformation). Me
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7

DePristo, Mark Andrew. "Ab initio conformational sampling for protein structure determination, analysis, and prediction." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615942.

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8

Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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9

Shi, Jingming. "Ab initio prediction of crystalline phases and their electronic properties : from ambient to extreme pressures." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1110/document.

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Dans cette thèse nous utilisons des méthodes globaux de prédiction des structures cristallographiques combinés à des techniques de grande capacité de traitement de données afin de prédire la structure cristalline de différents systèmes et dans des conditions thermodynamiques variées. Nous avons réalisé des prédictions structurales utilisant l'analyse cristalline par optimisation par essaims particuliers (CALYPSO) combinés avec la Théorie Fonctionnel de la Densité (DFT) ce qui a permis de mettre en évidence la stabilité de plusieurs composés jusqu'à la inconnus dans le digramme de phases du sys
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10

McLean, Malcolm Arthur. "Potential energy functions and search routines for ab initio protein structure prediction." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.522963.

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11

Chan, Maria Kai Yee. "Atomistic and ab initio prediction and optimization of thermoelectric and photovoltaic properties." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/53198.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2009.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 123-130).<br>The accurate prediction of physical properties in the vast spaces of nanoscale structures and chemical compounds is made increasingly possible through the use of atomistic and ab initio computation. In this thesis we investigate lattice thermal conductivities KL and electronic band gaps E,, which are relevant to thermoelectric and photovoltaic applications, respectively, and develop or modify computational tools for pre
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12

De, Bakker Paul I. Wen. "Ab initio sampling of polypeptide conformations and the prediction of protein structure." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619861.

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13

Kashiwabara, Andre Yoshiaki. "MYOP: um arcabouço para predição de genes ab initio\"." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-25112009-151237/.

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A demanda por abordagens eficientes para o problema de reconhecer a estrutura de cada gene numa sequência genômica motivou a implementação de um grande número de programas preditores de genes. Fizemos uma análise dos programas de sucesso com abordagem probabilística e reconhecemos semelhanças na implementação dos mesmos. A maior parte desses programas utiliza a cadeia oculta generalizada de Markov (GHMM - generalized hiddenMarkov model) como um modelo de gene. Percebemos que muitos preditores têm a arquitetura da GHMM fixada no código-fonte, dificultando a investigação de novas abordagens. Dev
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14

Mayo, Martin. "Ab initio anode materials discovery for Li- and Na-ion batteries." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/270545.

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This thesis uses first principles techniques, mainly the ab initio random structure searching method (AIRSS), to study anode materials for lithium- and sodium- ion batteries (LIBs and NIBs, respectively). Initial work relates to a theoretical structure prediction study of the lithium and sodium phosphide systems in the context of phosphorus anodes as candidates for LIBs and NIBs. The work reveals new Li-P and Na-P phases, some of which can be used to better interpret previous experimental results. By combining AIRSS searches with a high-throughput screening search from structures in the Inorga
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15

Zhu, Wenhan. "Improvement of ab initio methods of gene prediction in genomic and metagenomic sequences." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33869.

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A metagenome originated from a shotgun sequencing of a microbial community is a heterogeneous mixture of rather short sequences. A vast majority of microbial species in a given community (99%) are likely to be non-cultivable. Many protein-coding regions in a new metagenome are likely to code for barely detectable homologs of already known proteins. Therefore, an ab initio method that would accurately identify the new genes is a vitally important tool of metagenomic sequence analysis. However, a heuristic model method for finding genes in short prokaryotic sequences with anonymous origin was pr
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16

Gibbs, Nicholas. "Ab initio protein tertiary structure prediction using restricted ramachandran geometries and physio-chemical potentials." Thesis, University of Bristol, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340353.

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17

Sarmiento, Pérez Rafael. "Ab initio prediction of crystalline phases and electronic properties of alloys and other compounds." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10155/document.

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La thèse présente une étude dans le cadre de la conception ab initio de nouveaux matériaux, avec des applications aux alliages intermétalliques et semi-conducteurs, aux oxydes transparents conducteurs et aux solides moléculaires. Des simulations avec la méthode Minima Hopping combinée avec la théorie de la fonctionnelle de la densité ont été utilisées pour trouver des nouveaux composés dans les diagrammes de phase des composés binaires de Lithium-Aluminium et Sodium-Or, aussi bien que des géométries de faible symétrie de CuBO2 à plus basses énergies que la structure delafossite qui était consi
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18

Parra, Farré Genís. "Computational identification of genes: ab initio and comparative approaches." Doctoral thesis, Universitat Pompeu Fabra, 2004. http://hdl.handle.net/10803/7082.

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El trabajo que aquí se presenta, estudia el reconocimiento de las señales que delimitan y definen los genes que codifican para proteínas, así como su aplicabilidad en los programas de predicción de genes. La tesis que aquí se presenta, también explora la utilitzación de la genómica comparativa para mejorar la identificación de genes en diferentes especies simultaniamente. También se explica el desarrollo de dos programas de predicción computacional de genes: geneid y sgp2. El programa geneid identifica los genes codificados en una secuencia anónima de DNA basandose en sus propiedades intrínsec
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19

Laury, Marie L. "Accurate and Reliable Prediction of Energetic and Spectroscopic Properties Via Electronic Structure Methods." Thesis, University of North Texas, 2013. https://digital.library.unt.edu/ark:/67531/metadc500071/.

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Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space,
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20

Bonneau, Richard A. "Gene annotation using Ab initio protein structure prediction : method development and application to major protein families /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/9241.

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21

Markov, Maksim. "Prediction of thermal conductivity and strategies for heat transport reduction in bismuth : an ab initio study." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLX010/document.

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Cette thèse de doctorat porte sur l'étude théorique de la conductivité thermique du réseau dans le bismuth semi-métallique et sur les stratégies pour réduire la conductivité thermique en vue d'applications pour réduire l'échauffement dans les circuits électroniques, et pour la thermoélectricité. J'ai utilisé des méthodes avancées de résolution de l'équation de transport de Boltzmann pour les phonons, et de calcul ab initio des éléments de matrice de l'interaction phonon-phonon. J'ai calculé la dépendance en température de la conductivité thermique du réseau dans le matériau en volume en excell
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22

Brasil, Christiane Regina Soares. "Algoritmo evolutivo de muitos objetivos para predição ab initio de estrutura de proteínas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-20072012-163056/.

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Este trabalho foca o desenvolvimento de algoritmos de otimização para o problema de PSP puramente ab initio. Algoritmos que melhor exploram o espaço de potencial de soluções podem, em geral, encontrar melhores soluções. Esses algoritmos podem beneficiar ambas abordagens de PSP, tanto o modelo ab initio quanto os baseados em conhecimento a priori. Pesquisadores tem mostrado que Algoritmos Evolutivos Multiobjetivo podem contribuir significativamente no contexto do problema de PSP puramente ab initio. Neste contexto, esta pesquisa investiga o Algoritmo Evolutivo Multiobjetivo baseado em Tabelas a
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23

Griffiths, Mark. "Towards ligand design : Quantum Chemical Topology descriptors of heterocyclic compounds and pKa prediction from ab initio bond lengths." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/towards-ligand-design-quantum-chemical-topology-descriptors-of-heterocyclic-compounds-and-pka-prediction-from-ab-initio-bond-lengths(cea30196-c1ce-4801-b6d9-c81c330ae7e4).html.

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Bioisosterism is a field that is widely applied to biological molecules, including drugs and agrochemicals. Bioisosterism is the replacement of an active fragment in a molecule with another fragment similar in activity. The replacement is designed to alter the behavior of the molecule in its target environment. In previous work a bioisostere database called the Quantum Isostere Database (QID) was built out of descriptors derived from the theory of Quantum Chemical Topology (QCT). The current work aims to expand the existing QID to include ring fragments. A series of rings were characterised by
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24

Bonetti, Daniel Rodrigo Ferraz. "Algoritmos de estimação de distribuição para predição ab initio de estruturas de proteínas." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-03082015-193613/.

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As proteínas são moléculas que desempenham funções essenciais para a vida. Para entender a função de uma proteína é preciso conhecer sua estrutura tridimensional. No entanto, encontrar a estrutura da proteína pode ser um processo caro e demorado, exigindo profissionais altamente qualificados. Neste sentido, métodos computacionais têm sido investigados buscando predizer a estrutura de uma proteína a partir de uma sequência de aminoácidos. Em geral, tais métodos computacionais utilizam conhecimentos de estruturas de proteínas já determinadas por métodos experimentais, para tentar predizer proteí
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25

Lv, Duchao. "A Multi-Scale Simulation Approach to Deformation Mechanism Prediction in Superalloys." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1469009668.

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26

Čančarević, Željko P. "Prediction of not-yet-synthesized solids at extreme pressures, and the development of algorithms for local optimization on ab-initio level." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-28944.

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27

Faccioli, Rodrigo Antonio. "Implementação de um framework de computação evolutiva multi-objetivo para predição Ab Initio da estrutura terciária de proteínas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/18/18153/tde-09052013-145839/.

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A demanda criada pelos estudos biológicos resultou para predição da estrutura terciária de proteínas ser uma alternativa, uma vez que menos de 1% das sequências conhecidas possuem sua estrutura terciária determinada experimentalmente. As predições Ab initio foca nas funções baseadas da física, a qual se trata apenas das informações providas pela sequência primária. Por consequência, um espaço de busca com muitos mínimos locais ótimos deve ser pesquisado. Este cenário complexo evidencia uma carência de algoritmos eficientes para este espaço, tornando-se assim o principal obstáculo para este tip
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28

Kashiwabara, André Yoshiaki. "MYOP/ToPS/SGEval: Um ambiente computacional para estudo sistemático de predição de genes." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-02042012-184145/.

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O desafio de encontrar corretamente genes eucarioticos codificadores de proteinas nas sequencias genomicas e um problema em aberto. Neste trabalho, implementamos uma plata- forma, com o objetivo de melhorar a forma com que preditores de genes sao implementados e avaliados. Tres novas ferramentas foram implementadas: ToPS (Toolkit of Probabilistic Models of Sequences) foi o primeiro arcabouco orientado a objetos que fornece ferramentas para implementacao, manipulacao, e combinacao de modelos probabilisticos para representar sequencias de simbolos; MYOP (Make Your Own Predictor) e um sistema que
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29

Bonetti, Daniel Rodrigo Ferraz. "Aumento da eficiência do cálculo da energia de van der Waals em algoritmos genéticos para predição de estruturas de proteínas." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-20052010-110415/.

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As proteínas são moléculas presentes nos seres vivos e essenciais para a vida deles. Para entender a função de uma proteína, devese conhecer sua estrutura tridimensional (o posicionamento correto de todos os seus átomos no espaço). A partir da estrutura de uma proteína vital de um organismo causador de uma doença é possível desenvolver fármacos para o tratamento da doença. Para encontrar a estrutura de uma proteína, métodos biofísicos, como Cristalografia de Raio-X e Ressonância Nuclear Magnética têm sido empregados. No entanto, o uso desses métodos tem restrições práticas que impedem a determ
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30

Tuček, Jaroslav. "Předpovídání struktury proteinů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2009. http://www.nusl.cz/ntk/nusl-236732.

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This work describes the three dimensional structure of protein molecules and biological databases used to store information about this structure or its hierarchical classification. Current methods of computational structure prediction are overviewed with an emphasis on comparative modeling. This particular method is also implemented in a proof-of-concept program and finally, the implementation is analysed.
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31

Kulkarni, Aniket [Verfasser], and Martin [Akademischer Betreuer] Jansen. "Structure prediction of lithium, calcium carbide, and (per)nitride compounds at ambient and high pressure on the ab-initio level / Aniket Kulkarni. Betreuer: Martin Jansen." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2012. http://d-nb.info/102604328X/34.

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32

Harding, Alexander. "The prediction of mutagenicity and pKa for pharmaceutically relevant compounds using 'quantum chemical topology' descriptors." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/the-prediction-of-mutagenicity-and-pka-for-pharmaceutically-relevant-compounds-using-quantum-chemical-topology-descriptors(40e87ff2-e161-4f4c-9e90-3a4e9087dc9e).html.

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Quantum Chemical Topology (QCT) descriptors, calculated from ab initio wave functions, have been utilised to model pKa and mutagenicity for data sets of pharmaceutically relevant compounds. The pKa of a compound is a pivotal property in both life science and chemistry since the propensity of a compound to donate or accept a proton is fundamental to understanding chemical and biological processes. The prediction of mutagenicity, specifically as determined by the Ames test, is important to aid medicinal chemists select compounds avoiding this potential pitfall in drug design. Carbocyclic and het
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33

Bohonak, Noni McCullough. "Finding a Fitness Function to be Used with Genetic Algorithms to Solve a Protein Folding Problem: The ab initio Prediction of a Protein Using Torsion Angles." NSUWorks, 2000. http://nsuworks.nova.edu/gscis_etd/418.

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This dissertation shows that the ab initio prediction of a protein using torsion angles will work using the correct fitness function. It shows that work can be done on a high-end workstation using a small model of a protein. It was based on the previous work of Dr. Steffen Schulze-Kremer who received limited success with a faculty fitness function and a massively parallel system. The purpose of this work was to not only find the solution but to demonstrate how our rapidly advancing technology will permit this type of research to be moved from the costly parallel systems, nuclear magnetic reson
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34

Flores, Livas José. "Computational and experimental studies of sp3-materials at high pressure." Thesis, Lyon 1, 2012. http://www.theses.fr/2012LYO10127.

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Nous présentons des études expérimentales et théoriques de disiliciures alcalino-terreux, le disilane (Si2H6) et du carbone à haute pression. Nous étudions les disiliciures et en particulier le cas d’une phase plane de BaSI2 qui a une structure hexagonale avec des liaisons sp3 entre les atomes de silicium. Cet environnement électronique conduit à un gaufrage de feuilles du silicium. Nous démontrons alors une amélioration de la température de transition supraconductrice de 6 à 8.9 K lorsque les couches de silicium s’aplanissent dans cette structure. Des calculs ab initio basés sur DFT ont guidé
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Yao, Yongxin. "Thermodynamic prediction of glass formation tendency, cluster-in-jellium model for metallic glasses, ab initio tight-binding calculations, and new density functional theory development for systems with strong electron correlation." [Ames, Iowa : Iowa State University], 2009.

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36

Asthana, Abhishek. "Model Development and Application of Molecular Simulations for the Study of Proton Transport in Bulk Water and for the Prediction of Dipole Moments of Organic Compounds." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3389.

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The present work demonstrates the application of molecular simulations (MD) in two different areas: proton transport in bulk water and estimation of the dipole moment of polar organic compounds. In both areas, relatively few successful and robust methodologies exist. In the first part, a new polarizable water model is developed for MD simulations of the proton transport process. The model was parametrized from a combination of quantum chemical calculations and experimental water properties. The model was implemented in MD simulation studies of liquid water at room temperature, as well as with
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37

Mishra, Avdesh. "Effective Statistical Energy Function Based Protein Un/Structure Prediction." ScholarWorks@UNO, 2019. https://scholarworks.uno.edu/td/2674.

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Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D
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38

Lefèvre, Gauthier. "Propriétés physico-chimiques de nouveaux matériaux en couches minces pour le stockage d'hydrogène." Thesis, Artois, 2018. http://www.theses.fr/2018ARTO0406.

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Le stockage d'hydrogène est sans doute le dernier verrou au développement à grande échelle des piles à combustible. Utiliser l'hydrogène comme vecteur énergétique, produire efficacement de l'électricité sans avoir recours aux énergies fossiles et rejeter uniquement de l'eau, il s'agit là peut-être de la prochaine révolution technologique, écologique et qui signera la fin des problèmes environnementaux en terme d'énergie.L'hydrogène gazeux est dangereux et son stockage à l'état solide représente une solution mais au détriment de la quantité stockée et des conditions d'utilisation.Dans ce contex
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Votroubek, Lukáš. "Webový server pro predikci 3D struktury proteinu." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2013. http://www.nusl.cz/ntk/nusl-236225.

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This work deals with proteins, especially with their structure and kinds of tertiary, or 3D, structure prediction. Tertiary structure prediction is very important for function prediction of this vitally important substance. Bioinformatics do this prediction much more effective and faster, because classical methods of structure prediction directly from molecule are very expensive and slow. On the other hand they are much more exact. Objective of this thesis is to describe tertiary structure prediction methods, describe used tools and possibility of automatic communication with them.  Next objec
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40

Mooßen, Oliver [Verfasser], Michael [Gutachter] Dolg, and Michael [Gutachter] Hanrath. "Interpretation of ab initio Calculations of Cerium Compounds and Predictive Power of Density Functional Theory Calculations for Iodine Catalysis / Oliver Mooßen ; Gutachter: Michael Dolg, Michael Hanrath." Köln : Universitäts- und Stadtbibliothek Köln, 2018. http://d-nb.info/1162273518/34.

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41

Joubert, Pierre. "Inhomogeneites dues a la dependance en vitesse de la largeur et du deplacement collisionnels de h#2 et hf. Calculs ab initio et predictions des profils spectraux a haute temperature." Besançon, 1997. http://www.theses.fr/1997BESA2045.

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Ce travail est consacre a la comprehension des differents mecanismes collisionnels affectant les profils spectraux dans le cadre du diagnostic optique des milieux en combustion. Cette these est plus particulierement consacree a la determination des largeurs et deplacements des raies de h#2 et hf dans divers melanges (avec he, ar et n#2). Celle-ci est effectuee a partir de l'experience par ajustement avec des modeles cinetiques ou par des calculs ab initio a partir du potentiel intermoleculaire. Les spectres de hf perturbe par l'argon obtenus a basse pression presentent une asymetrie. Afin d'in
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42

Prascher, Brian P. "Systematic Approaches to Predictive Computational Chemistry using the Correlation Consistent Basis Sets." Thesis, University of North Texas, 2009. https://digital.library.unt.edu/ark:/67531/metadc9920/.

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The development of the correlation consistent basis sets, cc-pVnZ (where n = D, T, Q, etc.) have allowed for the systematic elucidation of the intrinsic accuracy of ab initio quantum chemical methods. In density functional theory (DFT), where the cc-pVnZ basis sets are not necessarily optimal in their current form, the elucidation of the intrinsic accuracy of DFT methods cannot always be accomplished. This dissertation outlines investigations into the basis set requirements for DFT and how the intrinsic accuracy of DFT methods may be determined with a prescription involving recontraction of th
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43

Aminpour, Maral. "Theoretical Studies of Nanostructure Formation and Transport on Surfaces." Doctoral diss., University of Central Florida, 2013. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/6239.

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This dissertation undertakes theoretical and computational research to characterize and understand in detail atomic configurations and electronic structural properties of surfaces and interfaces at the nano-scale, with particular emphasis on identifying the factors that control atomic-scale diffusion and transport properties. The overarching goal is to outline, with examples, a predictive modeling procedure of stable structures of novel materials that, on the one hand, facilitates a better understanding of experimental results, and on the other hand, provide guidelines for future experimental
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Tran, Thuong Van Du. "Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins." Phd thesis, Ecole Polytechnique X, 2011. http://tel.archives-ouvertes.fr/tel-00647947.

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Les protéines transmembranaires canaux-β (TMBs) se trouvent dans les membranes externes des bactéries à Gram négatif, des mitochondries ainsi que des chloroplastes. Elles traversent entièrement la membrane cellulaire et exercent différentes fonctions importantes. Vu qu'il y a un petit nombre des structures des TMBs déterminées, en raison des difficultés avec les méthodes expérimentales, il est douteux que ces approches puis- sent bien trouver et prédire les TMBs qui ne sont pas homologues avec celles connues. Nous construisons un modèle de graphe pour la classification et la prédiction de stru
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"Ab initio methods for protein structure prediction." Thesis, 2010. http://hdl.handle.net/1911/61957.

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Recent breakthroughs in DNA and protein sequencing have unlocked many secrets of molecular biology. A complete understanding of gene function, however, requires a protein structure in addition to its sequence. Modern protein structure determination methods such as NMR, cryo-EM and X-ray crystallography are woefully unable to keep pace with automated sequencing techniques, creating a serious gap between available sequences and structures. This thesis describes several ab initio computational methods designed in the near-term to facilitate structure determination experiments, and in the long-te
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46

Li, Shuai Cheng. "New Approaches to Protein Structure Prediction." Thesis, 2009. http://hdl.handle.net/10012/4846.

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Protein structure prediction is concerned with the prediction of a protein's three dimensional structure from its amino acid sequence. Such predictions are commonly performed by searching the possible structures and evaluating each structure by using some scoring function. If it is assumed that the target protein structure resembles the structure of a known protein, the search space can be significantly reduced. Such an approach is referred to as comparative structure prediction. When such an assumption is not made, the approach is known as ab initio structure prediction. There are several dif
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Liao, Min-Hung, and 廖敏宏. "Constructing Structural Model of Protein Functional Domains using ab initio Structure Prediction." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/20715227811664794191.

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碩士<br>國立臺灣大學<br>生物產業機電工程學研究所<br>96<br>The basic units of all kinds of organisms are proteins. In order to learn more about the protein function, scientists try to understand proteins from different points of view, including protein sequence, protein structure, location of functional residues, and so forth. In the fields of computational biology, the prediction of protein structure has always been the core issue that researchers indefatigably focus on. It has never been easy to tell the protein structure merely through protein sequence; hence methods for predicting the structures are being deve
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Pacheco, José Carlos Ribeiro. "PGP: prokaryote gene prediction software." Master's thesis, 2013. http://hdl.handle.net/1822/27894.

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Dissertação de mestrado em Bioinformática<br>A correta previsão e anotação de genes bacterianos é essencial para a aplicação da informação contida no ADN em muitos tópicos de pesquisa (bio)médica, como microbiologia, imunologia e doenças infeciosas. Embora existam vários softwares de previsão de genes bacterianos como GenemarkHMM, Glimmer e Prodigal e pipelines completos como ISGA, xBASE, Maker e Consensus Prediction, a previsão de genes pode ser melhorada. O principal objetivo deste trabalho foi o desenvolvimento de um pipeline de previsão de genes bacterianos, o Prokaryote Gene Prediction (P
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Ngoc, Quoc-Vu Ha [Verfasser]. "Protein structure and enzyme catalysis: knowledge-based protein loop prediction and ab initio equilibrium constant estimation / vorgelegt von Quoc-Vu Ha Ngoc." 2008. http://d-nb.info/989787516/34.

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Dal, Molin Alessandra. "Structural annotation of eukaryotic genomes in 2nd generation sequencing era." Doctoral thesis, 2016. http://hdl.handle.net/11562/940817.

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Nell'ultimo decennio, l'aumento dell’efficienza e la diminuzione del costo delle nuove tecniche di sequenziamento ha portato ad un accumulo di sequenze genomiche nei database pubblici. Con questa enorme quantità di sequenze a disposizione, la necessità di generare delle annotazioni precise e dettagliate non è mai stata così grande. L’annotazione strutturale del genoma è il processo di identificazione di elementi strutturali in una sequenza di DNA, classificandoli in base al loro ruolo biologico. L’approccio computazionale viene sempre più utilizzato per poter eseguire l'annotazione strutturale
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