Дисертації з теми "Molecular Structural Dynamics"
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Jiang, Nan. "Exploring Microtubule Structural Mechanics through Molecular Dynamics Simulations." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1504878667194719.
Повний текст джерелаGC, Jeevan. "Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins." FIU Digital Commons, 2017. http://digitalcommons.fiu.edu/etd/3225.
Повний текст джерелаWatson, Stuart. "Structural relaxation at defects by Ab initio molecular dynamics." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320648.
Повний текст джерелаKohlhoff, Kai Jochen. "Protein chemical shifts as structural restraints in molecular dynamics simulations." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612259.
Повний текст джерелаThalassinou, Joanne Frances. "Structural study of the adenylation domain by molecular dynamics simulation." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/66426/.
Повний текст джерелаWillems, Nathalie. "Molecular dynamics simulations of lipase-surface interactions." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:7765c334-7c02-4190-a4b2-99ad315cfe52.
Повний текст джерелаBateman, Neil. "Computer modelling and structural studies of phyllosilicate transformation during diagenesis and low grade metamorphism." Thesis, Keele University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273025.
Повний текст джерелаTuzun, Burcu. "Structural Properties Of Defected Graphene Nanoribbons Under Tension: Molecular-dynamics Simulations." Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614085/index.pdf.
Повний текст джерелаde, Manzanos Guinot Angela. "Structural studies of different form I Rubiscos using molecular dynamics simulations." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/51422.
Повний текст джерелаSigauke, Lester Takunda. "Structural studies on yeast eIF5A using biomolecular NMR and molecular dynamics." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1017927.
Повний текст джерелаMarino, Andrea. "Ultrafast investigation of electronic and structural dynamics in photomagnetic molecular solids." Thesis, Rennes 1, 2015. http://www.theses.fr/2015REN1S037/document.
Повний текст джерелаThe ability to photo-switch physical/chemical properties of functional materials through photo induced phase transition opens fascinating perspectives for driving the material towards new state out of thermal equilibrium. However, it is fundamental to disentangle and understand all the dynamical phenomena, otherwise hidden in statistically averaged macroscopic transformations. Arguably, time-resolved studies are unique approach to access the necessary information on the multiple degrees of freedom and elementary processes involved during the macroscopic switching. As photo-reversible molecular switches, spin crossover (SCO) materials are of particular interest. These photomagnetic and photochromic prototype materials undergo metastable photoinduced phase transition between two states of different spin multiplicity, namely low-spin (LS) and high-spin (HS). In this PhD work it will be presented the ultrafast electronic and structural dynamics of SCO molecular solids emphasizing the importance of using complementary probes sensitive to different degrees of freedom. The photoinduced spin state switching concerns initially only an ultrafast, but localized, molecular response which through strong electron-phonon coupling activates coherent intra-molecular vibrations. An ultrafast energy transfer from the molecule to the lattice, via phonon-phonon coupling, allows an efficient trapping of the system in the new photoinduced state. However in molecular solids, the excess of energy released from the absorber molecule results in a complex multi-scale aspect involving several degrees of freedom at different time scales. In this contest, we investigated the multi-step out-of equilibrium dynamics of a SCO system undergoing symmetry breaking between the HS phase and the intermediate (IP) phase where a long range ordering of HS and LS molecules results in a spin state concentration wave (SSCW), analogous to charge or spin density waves. Combined time-resolved X-ray diffraction and optical spectroscopy studies provide a complete overview of the out-of-equilibrium thermodynamics of the SSCW, investigating how the two order parameters describing the system evolve in time
Ince, Alper. "Investigation Of The Structural Properties Of Silicene Nanoribbons By Molecular Dynamics Simulations." Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614331/index.pdf.
Повний текст джерелаand 300 K°
temperatures by the aid of atomistic many-body potential energy functions. It has been found that under strain, SiNRs show such material properties: they are very ductile, they have considerable toughness and despite their low elasticity, they have a very long plastic range before fragmentation.
Steckmann, Timothy Michael. "Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2978.
Повний текст джерелаTamburrino, Giulia. "Structural characterization of bacterial membrane proteins via molecular dynamics simulations and electrophysiology." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/224d87fb-307f-49ba-82ec-e119b813e549.
Повний текст джерелаRenganathan, Ananthi. "Molecular Dynamics Simulation of transport and structural properties of molten reactor salts." The Ohio State University, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu161922120604859.
Повний текст джерелаBekele, Selemon. "Structural and Dynamical Properties of Water and Polymers at Surfaces and Interfaces: A Molecular Dynamics Investigation." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1530040420616781.
Повний текст джерелаSantoni, Gianluca. "Structural dynamics of acetylcholinesterase and its implications in reactivators design." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAY019/document.
Повний текст джерелаAcetylcholinesterase (AChE), one of nature fastest enzyme, is the target of multiple toxics,including organophosphate nerve agents (OP). In the first part of this thesis I present thestructure-based development of a new uncharged reactivator, which showed characteristicsbetter than any molecule commercially available to date. The molecule has been rationallydesigned to present both affinity to the inhibited enzyme and good reactivation capabilities.The interactions between the lead molecule KM297 and AChE has been characterizedby means of flexible docking, molecular dynamics simulations and X-ray protein crystallography.The deeper understanding of its binding modes to both native and OP-inhibitedAChE has helped in developing a derivative, JDS207, whose binding mode at the peripheralsite of AChE is optimized. This derivative has also been studied by flexible docking and Xraycrystallography. The design of this family of reactivators taught us that a deep insightof the AChE dynamics is necessary to optimize ligands. The second part of the thesis isdevoted to the analysis of molecular dynamics simulations of AChE. At first, we assessedthat combining multiple short simulations is a fast and reliable method to characterizethe dynamics of the amino-acids side-chains. By comparing dynamics of the side-chainsfrom hAChE and TcAChE, we confirm that some key dynamical differences exist betweenthe two enzyme. The knowledge of the rotamers issued of MD simulation has lead us todevelop a new method to generate flexible receptors for docking, which is specific to eachsingle residue in the enzyme. This method has been validated by comparing its outputstructures with the ones found on the PDB database
chen, xianfeng. "Interpretation and Prediction of Structural and Energetic Factors Controlling ABC Transporters." Digital Archive @ GSU, 2008. http://digitalarchive.gsu.edu/biology_diss/83.
Повний текст джерелаChiu, Liang-Yuan. "The Roles of RNA Structural Dynamics and Molecular Interaction in Viral Gene Expression." Case Western Reserve University School of Graduate Studies / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1625243374378648.
Повний текст джерелаScarabelli, G. "MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES: APPLICATIONS TO STRUCTURAL VACCINOLOGY AND PEPTIDE DESIGN." Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/150154.
Повний текст джерелаSoliman, Mahmoud E. S. "Computational modelling of glycosidase mechanisms : structural and mechanistic aspects." Thesis, University of Bath, 2009. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537489.
Повний текст джерелаTorsello, Mauro. "Structural and dynamic modeling of molecular systems at different length scales." Doctoral thesis, Università degli studi di Padova, 2016. http://hdl.handle.net/11577/3424405.
Повний текст джерелаLa continua crescita della potenza di calcolo, in termini di risorse hardware e software, ha reso l'approccio computazionale (in-silico) ai complessi problemi scientifici, uno strumento molto conveniente che permette di ottenere informazioni utili al fine di affiancare, interpretare ed, in alcuni casi, addirittura riprodurre i dati sperimentali a partire da principi primi. I metodi sono stati resi più veloci ed efficienti negli ultimi vent'anni, grazie anche allo sviluppo di algoritmi sempre più efficienti, in grado di sfruttare al meglio la potenza computazionale racchiusa nelle nuove soluzioni hardware (ad esempio architetture parallele basate sulle GPU), e di fornire pacchetti software di semplice utilizzo per molteplici applicazioni. Al giorno d'oggi l'approccio computazionale è impiegato in numerose aree scientifiche, che spaziano tra le più disparate discipline applicate come medicina, ingegneria, chimica, fisica, scienze dei materiali e molte altre. In particolare in questo lavoro di tesi, alcuni degli approcci della chimica computazionale quali meccanica quantistica, dinamica molecolare classica e metodi ibridi, sono applicati allo studio di biomolecole e macromolecole, al fine di investigare differenti aspetti come struttura, dinamica, energetica e in particolare la flessibilità. In aggiunta ai metodi su menzionati è stato anche esplorato un approccio fluido-dinamico al fine di descrivere e simulare sistemi microfluidici, focalizzando l'attenzione sulla reattività dei sistemi presi in esame. Tutti questi approcci sono dipendenti dall'estensione del sistema e, poiché hanno un differente costo computazionale, la loro applicazione dovrebbe essere limitata ad una ragionevole dimensione dei sistemi studiati. Le profonde differenze in termini di costo/accuratezza sono discusse, fornendo un collegamento tra le scale spaziali delle diverse metodologie, al fine di esplicare come le informazioni ottenute a scale spaziali inferiori possano essere considerate come punto di partenza accurato per effettuare simulazioni a scale spaziali maggiori, in un approccio che è oggi comunemente noto come modellazione multiscala. La connessione tra i metodi ad alta accuratezza/alto costo e quelli a bassa accuratezza/basso costo è commentata, illustrando così come un approccio multiscala possa permettere, in casi specifici, di incrementare al contempo l'accuratezza del dato calcolato e la dimensione del sistema simulato.
Slater, Craig Stephen. "Studies of photoinduced molecular dynamics using a fast imaging sensor." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:24b6edce-9bd0-4729-97d6-4de959618cb0.
Повний текст джерелаHafner, Melanie Salome [Verfasser]. "Structural conformational analysis of molecular dynamics of a P-glycoprotein homology model and generated intermediate structures / Melanie Salome Hafner." Bonn : Universitäts- und Landesbibliothek Bonn, 2019. http://d-nb.info/119893316X/34.
Повний текст джерелаTjhen, Richard June. "Structure and dynamics of ribonucleoproteins by X-ray crystallography and NMR: Structural basis of Piwi PAZ domain binding preference for 2'-O-methylated 3' terminal ssRNAs." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2010. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3398888.
Повний текст джерелаCaulfield, Thomas R. "Structural basis for the fidelity of translation modeling the accommodation pathway /." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/22553.
Повний текст джерелаCommittee Chair: Harvey, Stephen C; Committee Member: Hud, Nicholas V; Committee Member: Oyelere, Adegboyega; Committee Member: Wartell, Roger.
Sahakyan, Aleksandr B. "Extending the boundaries of the usage of NMR chemical shifts in deciphering biomolecular structure and dynamics." Thesis, University of Cambridge, 2012. https://www.repository.cam.ac.uk/handle/1810/243642.
Повний текст джерелаGardner, Adam R. "Molecular dynamics of aot/water/isooctane reverse micelles dynamic and structural analysis and effect of zirconium ions on the micelles structure for ZrO2 nanoparticle production /." abstract and full text PDF (free order & download UNR users only), 2007. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1442844.
Повний текст джерелаTavella, Davide. "Investigating the Contribution of Disordered Domains to the Biological Activity of RNA-binding Proteins." eScholarship@UMMS, 2018. https://escholarship.umassmed.edu/gsbs_diss/1005.
Повний текст джерелаSchneider, Violetta Franziska Roswitha [Verfasser], and M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
Повний текст джерелаSousa, Rui. "Structural insights of Interleukin-15 through Molecular Dynamics simulations : Towards the rational design of specific inhibitors." Thesis, Nantes, 2019. http://www.theses.fr/2019NANT4081.
Повний текст джерелаInterleukin 15 (IL-15) is a cytokine involved in a plethora of different cellular functions. It participates, for instance, in the development and activation of immune responses. IL-15 has, therefore, clearly appeared as a potential target for several therapeutic applications. The structure of this cytokine is based on a quaternary complex between IL-15 and its a (IL-15Ra), b ( IL-2Rβ) and y (yc) receptors. The key to the functional modulation of IL-15 lies on its interaction with its receptors and, more particularly, with IL-2Rβ. Interleukin-2 sharing two out of the three receptors 2Rβ and yc), the search for specific IL-15 inhibitors has to take into account these features. In this work, through various Molecular Modeling approaches, specifically Molecular Dynamics (MD) simulations, we have (i) determined the influence of the complexed form of IL-15 (dimer, trimer or tetramer) on the interface properties (ii) highlighted the key amino acid (“hot spots”) of the various interfaces (iii) studied the impact of mutations of selected residues (iv) used this information to design a pharmacophore which has allowed, in a subsequent step, the discovery of new low-molecular weight compounds able to specifically target one of the IL-15 interfaces (IL- 15/ IL-2Rβ). The theoretical data have been compared to the results of biological experiments carried out in the framework of the project
Schneider, Violetta [Verfasser], and M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
Повний текст джерелаHatta, Ichiro, Susumu Okazaki, Kimiko Oono, and Yoshimichi Andoh. "A molecular dynamics study of the lateral free energy profile of a pair of cholesterol molecules as a function of their distance in phospholipid bilayers." AIP Publishing, 2012. http://hdl.handle.net/2237/20839.
Повний текст джерелаDI, MARINO DANIELE. "Molecular dynamics and docking simulations of the ADP/ATP mitochondrial carrier: structural-dynamical insights for the inactivation of pathological mutants and detection of potential ATP binding sites." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2010. http://hdl.handle.net/2108/1174.
Повний текст джерелаThe mitochondrial adenosine diphosphate/adenosine triphosphate, ADP/ATP carrier (AAC) has been crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). The protein is composed by a six trans-membrane helix bundle, defining the nucleotide translocation pathway, that is closed towards the matrix side due to sharp kinks in the odd-numbered helices. The role of the protein is to import ADP in the mitochondrial matrix and export ATP in the cytosol. Several disease have been associated to a malfunctioning of the protein. To better understand the structural/dynamical properties of the carrier, two different computational experiments have been performed, in order to understand both the translocation mechanism and the role of known pathological mutations. In a first experiment Molecular Dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 20 ns to shed a light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues: Arg79, Asp134, Arg234; hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is completely lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network, as observed in the wild type, is restored. This causes a wrong assembly of the geometry of the binding site, explaining the impaired transport of the single mutant. Further, we describe the interaction between the matrix side of the AAC transporter and the ATP molecule using classical molecular dynamics simulation (MD) and protein-ligand docking procedure. From the 20 ns MD trajectory of the wild type protein, 15 structures have been extracted through clustering analysis and for each carrier conformation 50 docking runs have been carried out for a total of 750 (MD-docking). The results have been compared with 750 docking runs performed on the X-ray structure (X-docking). The docking procedure shows the presence of a single interaction site in the X-ray structure that is conserved in the structures extracted from the MD trajectory. MD-docking shows the presence of a second binding site, not found in the X-docking. The interaction strategy between the AAC transporter and the ATP molecule has been analyzed investigating the composition and 3D arrangement of the interaction pockets, together with the orientations of the substrate into them. A relationship between sequence repeats and the ATP binding sites in the AAC carrier structure is proposed.
Granero-García, Rubén. "Investigating the hydration and structural changes of molecular organic materials under high-pressure conditions." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://hdl.handle.net/11858/00-1735-0000-002B-7CB2-2.
Повний текст джерелаFonseca, James Ernest. "Temporal and steric analysis of ionic permeation and binding in Na+, K+-ATPase via molecular dynamic simulations." Ohio : Ohio University, 2008. http://www.ohiolink.edu/etd/view.cgi?ohiou1210868607.
Повний текст джерелаMajewski, Maciej. "Implications of Structural Stability for Drug Design." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/671195.
Повний текст джерелаChen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.
Повний текст джерелаCommittee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.
Becker, Simon [Verfasser]. "Structural studies on the outer membrane heme receptor of Serratia marcescens using molecular dynamics simulation / Simon Becker." Konstanz : Bibliothek der Universität Konstanz, 2012. http://d-nb.info/1028327811/34.
Повний текст джерелаReis, Renata Almeida Garcia. "Estudo dinâmico conformacional da proteína calgranulina C (S100A12) mediante interação com íons e receptor RAGE." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/60/60136/tde-03072012-163222/.
Повний текст джерелаCalgranulin C (S100A12) is a member of the S100 family of EF-hand calcium-binding proteins. Human S100A12 is predominantly expressed by granulocytes and is markedly overexpressed in inflammatory compartments. Elevated serum levels of S100A12 are found in patients suffering from various inflammatory, neurodegenerative, metabolic, and neoplasic disorders. Intracellular S100A12 exists as an anti-parallel homodimer. Each monomer is composed of a C-terminal, classic EF-hand (HI - LI - HII), an N-terminal, pseudo EF-hand (HIII - LIII - HIV). The motifs are linked by the hinge-region. Calgranulin C also binds zinc and copper ions in a site formed by both subunits of dimer. Changes in cytosolic ions concentrations regulate a wide variety of cellular process, and ions-binding proteins are the key molecules in signal transduction, differentiation, and cell cycle control. The mechanism by which calgranulin C modulates the course of inflammatory process is related to its interaction with the receptor for advanced glycated products (RAGE). In order to obtain details about the mechanism involved in cell signaling steps in which S100A12 participates, our goal was to qualify and quantify the activity conformational of S100A12 domains, induced by variations of intensive thermodynamic parameters, as changes in the concentration of ions. Furthermore we investigated the details of the interaction between S100A12 and RAGE in order to elucidate the region of the receptor which interacts with S100A12 and what are the residues involved in this interaction. In order to access the influence of the presence of ions over the conformational dynamics of S100A12, molecular dynamics simulations were performed using the GROMACS suite with the OPLS-AA force field and NVT ensemble. The initial structures used were experimentally determined by X-ray crystallography (PDB ID: 2WCE and 1E8A). They were separately submitted to different concentrations of sodium, calcium and zinc chloride and solvated with the SPC water model. Our results suggest that at low concentrations of Ca²?, LI remains occupied by Na?. During calcium-waves, it can reach the protein exclusively through LIII (in EF-2). As the Zn²? concentration rises, it contributes to the Na? unbinding from LI, an event that involves the residue ASP-25, which allows LI to open and the Na? to unbind. Furthermore, because of its high structural deformability, HIII is strongly influenced by both Na? and Ca²? ions which, in certain concentrations, leads to partial loss of this helix and of HIIa (Hinge-Region) and increases in the flexibility of this region, although only Ca²? is able to bind, through HIII, to the region near LIII. Regarding the RAGE studies, molecular docking essays and SMD (Steered Molecular Dynamics) simulations were performed. Our data analysis suggests that the interaction between S100A12 and RAGE takes place through both V and C1 RAGE domains and depends upon the interdomain region. Additionally, we observed that higher oligomeric states, e.g. S100A12 hexamers (PDB ID: 1GQM), have more interaction possibilites with RAGE and that, according to our results, in this case the interacting region of S100A12 comprises the N- and C-terminal portions of HI and Cterminal of HIV.
Hou, Shurong. "Structural Mechanism of Substrate Specificity In Human Cytidine Deaminase Family APOBEC3s." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1079.
Повний текст джерелаNguyen, Vu Quang. "Structural insights into the assembly and dynamics of the ATP-dependent chromatin-remodeling complex SWR1." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11606.
Повний текст джерелаJohansson, Robert. "Metal Hydrogen Interaction and Structural Characterization of Amorphous Materials from first principles." Doctoral thesis, Uppsala universitet, Materialteori, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-299940.
Повний текст джерелаPathmasiri, Wimal. "Structural and Biophysical Studies of Nucleic Acids." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8245.
Повний текст джерелаOkonogi, Tamara Mae. "Dynamics, thermodynamics, and structural investigations of nucleic acids using site-specific spin-labeling and electron paramagnetic resonance /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/8511.
Повний текст джерелаWhittington, Christi Leigh. "Molecular Dynamics of the RNA Binding Cavity of Influenza A Non-structural Protein 1 (NS1) RNA Binding Domain." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4256.
Повний текст джерелаYazdi, Samira [Verfasser], Michael [Akademischer Betreuer] Naumann, and Helmut [Akademischer Betreuer] Weiß. "The structural dynamics of soluble and membrane proteins explored through molecular simulations / Samira Yazdi ; Michael Naumann, Helmut Weiß." Magdeburg : Universitätsbibliothek, 2016. http://d-nb.info/111708597X/34.
Повний текст джерелаPatriksson, Alexandra. "From Solution into Vacuum - Structural Transitions in Proteins." Doctoral thesis, Uppsala : University Library Universitetsbiblioteket, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8300.
Повний текст джерелаCheerkapally, Raghavender P. "Surface-induced structural transformations in titanium nanowires." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384869599.
Повний текст джерелаUrquiza, Toledo María Laura. "Structural effects on the performance of 2D metal/semiconductor contacts and RRAM devices: first-principles and molecular dynamics studies." Doctoral thesis, Universitat Autònoma de Barcelona, 2020. http://hdl.handle.net/10803/671971.
Повний текст джерелаEn la presente tesis se estudiaron propiedades de transporte electrónico en uniones laterales metal-semiconductor de MoS2, usando funciones de Green de no equilibrio, destinadas a contactar canales 2D en transistores. Los resultados obtenidos contribuyeron a comprender la electrostática en uniones 2D. Además, la evaluación de diferentes geometrías de la interfaz metal-semiconductor permitió predecir las condiciones que proporcionan mejores propiedades de contacto. Estos estudios dieron lugar al desarrollo de un nuevo procedimiento para determinar los regímenes de emisión en uniones 2D metal-semiconductoras, experimental o teóricamente. Por otro lado, también se estudiaron dispositivos RRAM basados en HfO2 por medio de simulaciones de dinámica molecular, implementando un método de equilibración de carga que permite describir el efecto de un campo eléctrico externo, con lo cual se pudo caracterizar el proceso de "orming", "reset" y "set". A través del análisis de la migración de iones de oxígeno y el cambio en la coordinación de los átomos de Hf en el dieléctrico se pudo describir la formación y disolución de filamentos conductores durante el funcionamiento del dispositivo con un nivel de detalle sin precedentes. Estos estudios fueron complementados con cálculos de DFT de energías de formación y barreras de activación correspondientes a la migración de vacancias de oxígeno bajo el efecto de un campo eléctrico externo. Para obtener estos resultados, se propuso un novedoso esquema con el que es posible realizar cálculos DFT en materiales 2D, introduciendo carga neta y un campo externo. Finalmente, el fenómeno de "resistive swithching" en celdas RRAM basadas en MoS2 con electrodos de oro se estudió por medio de cálculos de transporte usando primeros principios, con el objetivo de dilucidar las estructuras responsables de los estados de alta y baja resistividad.
In this theis, finite bias transport properties of 2D MoS2 lateral metal-semiconductor junctions were studied through non-equilibrium Green's functions calculations, aimed at contacting the 2D channel in a field effect transistor. The obtained results contributed to the understanding of the electrostatics in 2D junctions. Besides, the evaluation of different interface geometries allowed to predict the conditions that provide better contacting properties. From these studies, we contributed with an improved procedure to determine, experimentally or theoretically, emission regimes in 2D metal-semiconducting junctions. Also, HfO 2 -based RRAM cells were studied using MD simulations with an extended charge equilibration method to describe external electric fields, which allowed to characterize the forming, reset and set processes. The analysis of the migration of oxygen ions and the change in the coordination of Hf atoms in the dielectric was used to describe the formation and dissolution of conductive filaments during the operation of the device with unprecedented detail. These studies were completed with DFT calculations of formation energies and activation barriers for the migration of oxygen vacancies, also obtained under the effect of an external electric field. In order to achieve such purpose, a novel scheme to perform calculations of slabs including a net charge and an electric field was proposed. Finally, resistive switching phenomena in MoS 2 monolayers sandwiched between Au electrodes was studied through DFT transport calculations, with the intent to elucidate the structure responsable for the high and low resistance states.
Universitat Autònoma de Barcelona. Programa de Doctorat en Enginyeria Electrònica i de Telecomunicació