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Dissertations / Theses on the topic 'Crystallography'
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1
Leech, Michael Andrew. "Supramolecular crystallography." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301231.
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Xie, Yong. "Maximum entropy in crystallography." Thesis, De Montfort University, 2003. http://hdl.handle.net/2086/4220.
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Barnard, Edward S. "AtomicControl : a crystallography simulator." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32853.
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Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2005.Includes bibliographical references (p. 51).
AtomicControl is a software package designed to aid in the teaching of crystallography and x-ray diffraction concepts to materials science students. It has the capability to create an arbitrary crystal structure based on the user's specification of a space group and atomic coordinates. It also can generate a simulated powder diffractogram based on the user's generated crystal. The program is fully interactive and allows the user to view the effects of changes to lattice and atoms in a 3D visualization of the crystal. AtomicControl's x-ray diffraction patterns have been shown to match well with experimental data, proving the validity of the algorithm. AtomicControl is available online.
by Edward S. Barnard.
S.B.
4
Ellis, Matthew James. "Electron crystallography of soluble proteins /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3549-1/.
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Kinna, David John. "Pattern recognition in chemical crystallography." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318724.
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Boyce, Geraldine. "Electron crystallography of organic pigments." Thesis, University of Glasgow, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340747.
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Gilmore, C. J. "The phase problem in crystallography." Thesis, University of Glasgow, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321995.
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Henderson, R. K. "Some theoretical aspects of crystallography." Thesis, University of York, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.377279.
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Lolis, Elias. "Crystallography and mutogenesis triosephosphate isomerase." Thesis, Massachusetts Institute of Technology, 1990. http://hdl.handle.net/1721.1/13959.
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Kerr, Hannah Elin. "NMR crystallography of disordered cocrystals." Thesis, Durham University, 2017. http://etheses.dur.ac.uk/12037/.
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Crystallographic disorder is common in the solid state but it is rarely investigated explicitly despite having a fundamental impact on the solid-state structure of a material. In this work, nuclear magnetic resonance (NMR) crystallography methods are utilised to achieve a detailed understanding of the structure and dynamics of solid organic systems containing disorder. Several new cocrystal systems are studied, each containing a topical drug molecule (caffeine, naproxen or furosemide) and each serving to demonstrate how NMR crystallography can be applied to a variety of structural questions. Hydrogen bonding motifs are identified using single crystal X-ray diffraction experiments, where possible, and are subsequently verified by solid-state NMR. Alternative hydrogen bonding models are ruled out by comparison of experimental solid-state NMR data with density functional theory calculated shieldings, and proton transfer can be investigated by monitoring the energy of the system with respect to proton position. In a particularly challenging case, 2D solid-state NMR experiments go some way to identify the hydrogen bonds in a system that cannot be crystallised. Dynamic disorder of fragments and solvent molecules are characterised by variable temperature solid-state NMR, including analysis of relaxation times to establish energy barriers and rates of motion. A mechanism of motion is also proposed for dynamic acetone molecules in a new cocrystal solvate, which is supported by good agreement between experimental and simulated 2H static NMR line shapes. Finally, the current limit of NMR crystallography is identified with respect to the reproducibility of calculated NMR parameters following geometry optimisation. It is shown that the geometry optimisation protocol does not affect standard NMR crystallography investigations pertaining to atom assignment, but it is significant for cases where very subtle structural features are probed, such as NMR linewidths. Overall, NMR crystallography investigations allow a deeper understanding of solid materials to be achieved than would be possible with any single technique and this work highlights the applicability of such methods to complex materials containing disorder.
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Tourigny, David Scott. "Overcoming challenges in macromolecular crystallography." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708430.
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Maehigashi, Tatsuya. "Ultra-high resolution DNA crystallography." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29684.
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Thesis (Ph.D)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.Committee Chair: Williams, Loren; Committee Member: Bottomley, Lawrence; Committee Member: Hud, Nicholas; Committee Member: Oyelere, Adegboyega; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Ishiyama, Noboru. "Electron crystallography of myelin basic protein." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ56331.pdf.
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Clifton, Ian Jeffrey. "Laue crystallography of proteins and viruses." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316825.
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Ralph, Adam Charles. "Physical and direct methods in crystallography." Thesis, University of York, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304487.
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Casadei, Cecilia Maria. "Neutron crystallography of a heme peroxidase." Thesis, University of Leicester, 2015. http://hdl.handle.net/2381/33365.
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Heme peroxidases are an ubiquitous family of catalytic iron-containing proteins. These enzymes are responsible for the catalysis of hydrogen peroxide removal from the cell through the formation of high valent transient states of the heme cofactor. The purpose of the present research project is to investigate the reaction pathway of cytochrome c peroxidase. The study of hydrogen related chemical features in the active site of this enzyme in the resting state and in the transient species is of paramount importance for the clarification of the reaction mechanism. In these circumstances neutron crystallography is the technique of choice. Neutron crystallography allows the direct localization of deuterium substituted hydrogen atoms in macromolecules in absence of radiation-induced damage. The structures of the resting state and of cryo-trapped compound I of cytochrome c peroxidase were determined by neutron crystallography. The nature of the catalytic center was investigated and in particular the protonation state of the heme iron axial ligand and of the key catalytic residues was established. These findings contributed to the understanding of the reaction pathway from the resting state to the intermediate species compound I. Complementary spectroscopic techniques were employed to assess compound I formation in single crystals and its stability in the conditions of the neutron crystallography experiment. The temperature dependence of the key catalytic features of cytochrome c peroxidase in the resting state was investigated by neutron crystallography. Significant alterations of protonation states were found in the resting state at cryogenic temperature. In addition the nature of the heme iron distal ligand was found to be affected by temperature in the resting state and it was possible to relate this phenomenon to the temperature induced spin state change observed by spectrophotometry in the visible region. As part of the present project, contribution was given to the development of the cryogenic temperature sample environment at the neutron macromolecular diffractometer LADI-III of the Institut Laue-Langevin broadening the experimental capabilities of the instrument. A wide range of experiments are made possible by the new set-up including the cryo-trapping of catalytic intermediates, the study of the temperature dependence of structural features and the investigation of species and complexes that are not stable at ambient temperature.
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Anderson, Megan J. Quake Stephen R. Quake Stephen R. "Microfluidics-based strategies for protein crystallography /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-10172008-222221.
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Yang, Ding-Shyue (Jerry) McKoy Vincent Zewail Ahmed H. "Ultrafast electron crystallography: principles and applications /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-05082009-170032.
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Tosi, Giovanna <1979>. "Macromolecular crystallography: crystallisation and structural determination." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1625/1/TESI_GT.pdf.
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Tosi, Giovanna <1979>. "Macromolecular crystallography: crystallisation and structural determination." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1625/.
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Mifsud, Richard William. "An exploration of some aspects of molecular replacement in macromolecular crystallography." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/282871.
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This thesis reports work in three areas of X-ray crystallography. An initial chapter describes the structure of a protein, the methods based on the use of X-rays and computer analysis of diffraction patterns to determine crystal structure, and the subsequent derivation of the structure of part or all of a protein molecule. Work to determine the structure of the protein cytokine receptor-like factor 3 (CRLF3) leading to the successful generation of a structural model of a significant part of this molecule is then described in Chapter 2. A variety of techniques had to be deployed to complete this work, and the steps undertaken are described. Analysis was performed principally using phaser, using maximum likelihood methods. Areas for improvement in generating non-crystallographic symmetry (NCS) operators in existing programmes were identified and new and modified algorithms implemented and tested. Searches based on improved single sphere algorithms, and a new two-sphere approach, are reported. These methods showed improvements in many cases and are available for future use. In Chapter 4, work on determining the relative importance of low resolution and high intensity data in molecular replacement solutions is described. This work has shown that high intensity data are more important than the low resolution data, dispelling a common perception and helping in experimental design.
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Carlsson, Gunilla. "Crystallography in Four Dimensions : Methods and Applications." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4301.
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Dean, Christopher. "Crystallography of transformation mechanisms in inorganic compounds /." Title page, contents and abstract only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phd281.pdf.
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Zheleva, Zhasmina Vasileva. "Surface crystallography of complex and disordered surfaces." Thesis, University of Reading, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.553057.
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O'Connor-Farbiarz, Melissa. "Overcoming the bottleneck phases in protein crystallography." Thesis, University of Liverpool, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533950.
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Wall, Clare. "Mathematical methods in protein x-ray crystallography." Thesis, University of York, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403863.
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Sharma, Rishi Ph D. Massachusetts Institute of Technology. "The crystallography of three flavor quark matter." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/45393.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2007.Includes bibliographical references (p. 197-209).
The nature of cold three-flavor quark matter at the large (but not asymptotic) densities relevant to neutron star phenomenology is not resolved. The gapless CFL phase, which was previously believed to have the lowest free energy, was recently shown to be unstable in the sense that some phase must have lower free energy. The nature of the instability motivates the hypothesis that the stable phase is a crystalline color superconductor. In this thesis, we present the calculation of the free energies of three-flavor crystalline color superconductors for realistic crystal structures in the Ginzburg-Landau approximation. All previous work on this subject neglected the strange quarks; we include them, with qualitative consequences. We calculate free energies for many crystal structures, and find two (based upon cubic symmetry) that have lower free energy than the gapless CFL phase over the lower density half of the relevant parameter space. They are therefore good candidates for the phase quark matter exists in, if it is present in the cores of neutron stars. We investigate the implications of the existence of a crystalline color superconducting core on the phenomenology of glitches in neutron stars. The key ingredient in the standard explanation of the origin of glitches is the presence of a rigid lattice in a superfluid medium which provides sites where vortices in the superfluid can be pinned, a situation that exists in the inner crust of the neutron stars. By deriving the effective action of the phonons in the crystalline phases, we determine that these are very rigid, with a shear modulus 20 to 1000 times larger than that of neutron star crusts. They are at the same time superfluid and a rough estimate of the pinning force on vortices gives answers comparable to that for pinning in the inner crust. This raises the possibility that (some) glitches could originate in quark matter cores of neutron stars.
by Rishi Sharma.
Ph.D.
28
Lee, Rachael. "Extreme conditions crystallography of polymorphic co-crystals." Thesis, Durham University, 2017. http://etheses.dur.ac.uk/12065/.
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This work has two principal sections. The first section is a study of the hydrogen bonding in a series of urea inclusion compounds, utilising neutron diffraction methods and a novel technique for growing neutron diffraction-suitable single crystals. The second section focusses on high pressure crystallography as a technique for exploring polymorphic landscapes, of a series of acid-base co-crystals, and the well-known active pharmaceutical ingredient 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY). Single crystal neutron structures at several temperatures have been determined for -phase urea inclusion compounds containing hexadecane, 1,6-dibromohexane and 2,7-octanedione guests. The neutron structure of the ‘partial channel’ co-crystal of urea and DMF is also reported. This includes an in-depth discussion and analysis of the structure and bonding of this urea series, in particular, how the guest compound affects the symmetry and hydrogen bonding of the host urea network. Additionally, the challenge of obtaining crystals suitable for neutron diffraction is addressed and a new heating/cooling device to aid crystallisation is presented. Pyridine and formic acid have been crystallised at differing ratios by both cryo-crystallisation and compression in a diamond anvil cell. Mixtures of the liquids in 1:1, 1:2 and 1:4 ratios all crystallise at high pressure, while only the 1:1 and 1:4 compositions were crystallised by in situ low temperature capillary crystallisation. The 1:2 structure crystallised by high pressure is a previously unknown co-crystal of pyridine - formic acid. For the 1:4 mixture, a new polymorph has been identified at a pressure of 14.2 kbar with a distinctly different structure and bonding pattern to that of the previously reported low temperature form. Five new co-crystals of 2,6-dimethylpyridine (DMP) with formic acid (FA) were crystallised by application of pressure in a diamond anvil cell and by in situ cryo-crystallisation. Mixtures in ratios 1:1, 1:2 and 1:3 of DMP: FA have been crystallised via both methods. Both the 1:2 and 1:3 co-crystals exhibit high pressure/low temperature polymorphism. ROY has been crystallised from acetone solution using a diamond anvil cell. The needle-like form obtained, named ONP shows similarities with the ORP, ON and Y forms, determined by Raman spectroscopy. The ONP crystals were recovered from the pressure cell by freezing with liquid nitrogen. Synchrotron X-ray data were collected on the sample, although no structure solution and refinement was possible. The unit cell of the ONP shows a crystallographic relationship to the ORP form.
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Gerstel, Markus. "Radiation damage in protein crystallography : susceptibility study." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:be55baee-19b7-4a34-8694-fb9c3606a19c.
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Protein structure models obtained from X-ray crystallography are subject to radiation damage. The resulting specific alterations to protein structures can be mistaken for biological features, or may obscure actual protein mechanisms, leading to misidentification or obscuration of biological insight. The radiation chemistry behind this site-specific damage is not well understood. Radiation damage processes progress in proportion to the dose absorbed by the crystal in the diffraction experiment. Doses can be estimated using existing software, but these assume idealised experimental conditions. To simulate complex diffraction experiments, including treatment of imperfect X-ray beam profiles and inhomogeneous dose distributions, a new program, RADDOSE-3D, was developed. RADDOSE-3D can be integrated into beamline software to provide convenient, more accurate, comparative, and publishable dose figures, also facilitating informed data collection decisions. There is currently no method to automatically detect specific radiation damage in protein structure models in the absence of an 'undamaged' reference model. Radiation damage research therefore generally relies on detailed observation of a few model proteins. A new metric, BDamage, is designed and used to identify and quantify specific radiation damage in the first large-scale statistical survey of 2,704 published protein models, which are examined for the effects of local environments on site-specific radiation damage susceptibility. A significant positive correlation between susceptibility and solvent accessibility is identified. Current understanding of radiation damage progression is mostly based on a few consecutive structure model 'snapshots' at coarse dose intervals. The low sampling rate considerably limits the ability to identify varying site susceptibility and its causes. Real space electron density data are obtained for crystals of different mutants of a RhoGDI protein with very high sequence identity, to determine sensitising and stabilising factors for radiation induced structural changes. Utilising a newly developed data collection and analysis protocol, these changes could be tracked with unprecedented time resolution.
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Stewart, Andrew A. "Developments in structure solution for electron crystallography." Thesis, University of Glasgow, 2003. http://theses.gla.ac.uk/30828/.
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The concept of electron crystallography is by no means new, although the majority of crystallographers will never have contemplated trying the technique, to solve a structural problem. Electron crystallography is fraught with problems from sample preparation, and data collection to structure solution, all have unique and challenging problems when being used in the context of electron crystallography. New techniques and methodologies for structure solution using electron crystallographic data are presented with the aim of making structure solution a more routine part of the procedure for electron crystallography. The problems of phase extension into the missing cone region, structure solution and refinement of the structures are all dealt with here.
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Ginn, Helen. "Improved methods for serial femtosecond crystallography reduction." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:a69f65b8-84d9-4c3a-84b9-155ded0e5dee.
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X-ray free electron lasers (XFELs) are a young technology which alleviates a number of issues, including radiation damage, which remain problematic in conventional macromolecular X-ray crystallography. As it turned out, existing methods had been optimised for synchrotron-based rotation data and coped poorly with snapshot XFEL diffraction images. In the first four results chapters, I present algorithms developed in my efforts to contribute to improved data reduction for XFEL analysis. In order of execution, these are: detector geometry refinement, indexing, initial orientation matrix refinement and post-refinement. Geometry refinement has been a field plagued with the problem of correlated parameters. I introduce the "slip-and-slide" algorithm to solve this by reparameterising detector movements based on their effect on diffraction. I developed an indexing algorithm, TakeTwo, to reduce diffraction pattern wastage by maximising information content on a single image. Initial orientation matrix refinement aims to reduce, without any prior reference, errors of a crystal model from its own information content. When an approximate solution is available, one may implement post-refinement, which, in combination with a model describing the partial illumination of each reflection, drives the model parameters towards a self-consistent data set. In the final results chapter, I present an example of how the combination of all of these algorithms can push the information quality to new levels, illustrated by merging XFEL diffraction collected from scarce quantities of bovine enterovirus type 2 crystals and demonstrating the power of the amplitudes to drive phase extension. I end the thesis with a discussion of the realistic impact of these algorithms, the directions that methods developer communities could take from here onwards, and my personal scientific direction for the future.
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Lequeu, Ph. "Comparison of crystallographic and continuum yield surfaces for textured polycrystals." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74039.
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Santoni, Gianluca. "Structural dynamics of acetylcholinesterase and its implications in reactivators design." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAY019/document.
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L’acétylcholinestérase (AChE), une des enzymes les plus rapides dans la nature, est lacible d’un large nombre de toxiques, dont notamment les neurotoxiques organophosphorés.La première partie de ce manuscrit de thèse décrit le développement raisonné d’un nouveauréactivateur, qui présente des propriétés de réactivation supérieures aux moléculesactuellement sur le marché. Les interactions entre cette molécule, KM297, et l’AChE ontété étudiées par dynamique moléculaire, docking et cristallographie aux rayons X. La connaissancedes modes de liaison du KM297 dans l’AChE native ou inhibé par un OP ontpermis de développer la molécule JDS207, qui se lie de façon exclusive au site périphériquede l’AChE. La deuxième partie de la thèse est dédiée à l’analyse des simulations de laAChE par dynamique moléculaire. On observe que la combinaison de multiples trajectoiresgénérées avec des paramètres de vélocité initiale différents est une méthode fiablepour caractériser les conformations atteintes par les chaînes latérales des acides aminés. Encomparant la distribution des rotamères pour l’AChE humaine et celle du poisson Torpedocalifornica, on montre que des différences importantes existent entre les enzymes des deuxespèces. A partir de ces informations sur les conformations de résidus clés du site actif,une méthode a été développée pour générer des récepteurs utilisable pour des calcules dedocking flexible, de façon à prendre en compte la dynamique propre à chaque résidu del’enzyme. Cette méthode a été validé en comparent les résultats obtenues à des structurescristallographiques connuesAcetylcholinesterase (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
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Meng, Guoyu. "Structural study of levansucrase by x-ray crystallography." Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403446.
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Shilova, Anastasiia. "Development of serial protein crystallography with synchrotron radiation." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY034/document.
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Le rayonnement synchrotron est l'un des facteurs clés du grand succès de la cristallographie macromoléculaire au cours des dernières décennies. Plus de 90% de toutes les structures de protéines de la base de données PDB a été résolu par cristallographie en utilisant des sources de rayonnement synchrotron et environ 95% d'entre elles a été déterminé à partir de cristaux congelés.Cependant, les structures déterminées par des techniques de congélation sont limitées par la nature statique des cristaux congelés. Avec le développement récent des sources de RX produites par lasers à électrons libres (XFEL), qui sont en mesure de produire des impulsions femtosecondes très intenses de rayons X, l'ère de la « diffraction avant destruction » et de la cristallographie sérielle femtoseconde utilisant des micro- ou nano- cristaux a commencé (SFX).Au cours du procédé SFX un cristal de protéine n'est exposé qu'une fois au faisceau de rayons X pendant quelques dizaines de femtosecondes avant qu'il ne soit complètement détruit. Les données sont collectées à partir de cristaux orientés de façon aléatoire par rapport au faisceau de rayons X; une seule exposition par cristal est possible. Afin de recevoir un ensemble de données plus complet, de nouvelles techniques d'analyse de données de diffraction ont été développées.La première expérimentation réussie du procédé (SFX) a été réalisée au LCLS à Stanford en décembre 2009 sur des cristaux du photosystème I et de lysozyme. Les experts en cristallographie des installations XFEL peuvent déterminer des structures de protéines à température ambiante presque exemptes de dégâts d'irradiation, en raison des pulses de FEL femtosecondes si brèves, qu'ils passent à travers l'échantillon avant que des dommages de rayonnement importants ne se produisent.Après la présentation des premières expériences SFX réussies, des efforts pour effectuer une cristallographie en série de cristaux de taille de l’ordre des micromètres à température ambiante ont commencé au sein des synchrotrons. Une première tentative de cristallographie synchrotron en série et à température ambiante a été tentée à PETRA III à DESY à Hambourg. Cette méthode a été nommée SMX (synchrotron serial millisecond crystallography), où des milliers d'échantillons sont collectés à partir de cristaux individuels passant par le faisceau à rayons X. Avec le développement des techniques de cristallographie série à température ambiante au sein des synchrotrons, la répartition de la dose sur un grand nombre de cristaux compense l’augmentation des dommages liés à l’irradiation à température ambiante.Bien que les sources de rayonnement synchrotron n'atteindront probablement jamais la même luminosité que les impulsions de rayons X comme dans les XFELs, elles ont un certains nombre d'avantages. L'un d'eux est la flexibilité de configuration grâce au paramétrage de lignes de faisceaux microfocus. Un autre est que plusieurs expositions par cristal sont possibles. En outre, les synchrotrons sont plus répandus dans le monde: la probabilité d'obtenir un temps d'expérimentation dans un synchrotron est plus élevée que pour une installation XFEL. En effet, maintenant deux installations XFEL sont ouvertes pour les utilisateurs .L'objectif de cette thèse est de proposer et de mettre en œuvre des méthodes qui permettront de recueillir des données en utilisant l'approche de la cristallographie série à l'installation synchrotron européen (ESRF, Grenoble, France). Cette thèse présente différentes techniques pour réaliser la cristallographie sérielle sur la ligne ID13 à l’ESRF. L'objectif était de développer la cristallographie sérielle sur synchrotron basée sur la numérisation micro-diffraction pour démontrer que les sources de rayonnement synchrotron peuvent être utilisées comme un instrument de routine pour cette technique avec des protéines globulaires et membranaires. Les aspects de la collecte de données et leur traitement seront également discutésSynchrotron radiation is one of the key factors for the tremendous success of macromolecular crystallography during the past decades. More than 90 % of all protein structures in PDB database were solved by crystallography using synchrotron radiation sources and around 95 % of them were determined from cryocooled crystals1,2. A whole data set can be collected from one flash-cooled crystal. Data-collection at cryogenic temperatures drastically reduces radiation damage effects. However, structures determined using cryo freezing techniques are limited by static nature of frozen crystals.With the recent development of X-ray free-electron laser facilities (XFELs), which are able to produce extremely intense femtosecond X-ray pulses, the era of “Diffraction before destruction” and serial femtosecond crystallography (SFX) for micro-/nano-sized crystals has begun3. In the SFX technique a protein crystal is only exposed once to the X-ray beam for tens of femtoseconds before it is completely destroyed. The data is collected from randomly oriented crystals that are exposed to the X-ray beam; only one shot per crystal is possible. In order to receive a complete data set, new data analysis techniques that are capable of dealing with large quantities of diffraction data have been developed. First experiment where serial femtosecond crystallography (SFX) approach was first carried out was performed at the Linac Coherent Light Source (LCLS, Stanford, USA) in December 2009 on photosystem I and lysozyme crystals4,5,6. At XFELs facilities crystallographers can perform room temperature structure determination of proteins almost free of radiation damage, due to the fact that femtosecond flashes of FEL is so brief, that it passes through the sample before the significant radiation damage occurs.After presenting first successful experiments with SFX technique, efforts to perform serial crystallography of micron-sized crystals at room-temperature started at synchrotron sources. First attempt to perform synchrotron room-temperature serial crystallography has been done at PETRA III at DESY in Hamburg using glass capillary based microfluidics7. This method was named synchrotron serial millisecond crystallography (SMX), where thousands of patterns are collected from individual crystals passing through the X-ray beam8. With development of room-temperature serial crystallography techniques at the synchrotrons, the exposure distributed on a large number of crystals in the sample, which helps compensating the effect of increased radiation damage at ambient temperature.Although synchrotron sources most certainly will never reach the same brightness of X-ray pulses like XFELs, they have some advantages. One of them is possibility to perform any set up due to the flexibility of the parameters of microfocus beamlines. Another advantage of SMX is that several shots per crystals are possible. Also should be mentioned that synchrotrons are more widespread all over the world, so possibility to get a beamtime at the synchrotron is much higher than at XFELs, because currently only two XFEL facilities are open for users (LCLS, USA and SACLA, Japan).The aim of this dissertation is to propose and to implement methods that will allow to collect data using the serial crystallography approach at the European synchrotron radiation facility (ESRF, Grenoble, France). This dissertation presents different techniques to perform synchrotron serial crystallography at ID13 beamline. The goal was to develop synchrotron serial crystallography based on scanning micro-diffraction to demonstrate that synchrotron sources can be used as a routine instrument to perform serial crystallography with soluble and membrane proteins. The aspects of the data collection and data processing also will be discussed
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Heller, Kyle Jeffrey. "CRYSTALLOGRAPHY OF TITANIUM BASED ORGANIC-INORGANIC HALIDE PEROVSKITES." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2798.
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Kyle Heller, for the Master of Science degree in Mechanical Engineering, presented on October 2020, at Southern Illinois University Carbondale.MAJOR PROFESSOR: Dr. Kanchan Mondal Using powder X-ray diffraction, a material can have its crystalline structure identified. Powder X-ray diffraction alone is not enough if a material is unknown. Usually the exact chemical formula of the material is known, or a secondary analytical method is used to extract additional data in order to analyze the crystalline structure using Bragg’s law and the interplanar relationships. Secondary analytical methods are not as easy or inexpensive though. Generic values could be placed into the more basic structure types to obtain a rough idea of potential crystal types including space groups for the material based on its diffraction peaks. However, with a material that has an unknown spacing between its atoms (d-spacing) this is harder to implement. Thus, the use of a secondary software was employed to further analyze the possibilities. In this thesis, the software used for data extraction and refining were Expo 2014 and CrystalMaker X paired with CrystalDiffract and the final visualization was achieved using Endeavor. Two different titanium based organic inorganic halide perovskites (Dye 3 and Dye 4) prepared at different temperatures were evaluated to identify the crystallographic structure using only x-ray data available. The crystal parameters were calculated, and potential unit cells were visualized. Both the materials were found to be 4 (ABX3) type perovskites. The organic component for Dye 3 was methyl ammonium ion and that of Dye 4 was formamidinium ion. These perovskites have shown potential for use as sensitizers in visible light photovoltaic cells. It was concluded that Dye 4 was orthorhombic with a space grouping of C m c a (space group 64). The associated values were a = b =7.94 Å and c =11.55 Å. Dye 3 was also found to be orthorhombic with space grouping of P c c n (space group 56) being a better fit than C m c a. The associated values were a=b=16 Å and c=11 Å.
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Salager, Elodie. "High-resolution solid-state NMR for powder crystallography." Lyon, Ecole normale supérieure, 2010. http://www.theses.fr/2010ENSL0592.
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La connaissance de la structure tridimensionnelle d’un composé solide est essentielle pour la compréhension de ses propriétés et le développement de nouveaux matériaux. La diffraction des rayons X est communément utilisée pour déterminer la structure des composés monocristallins. La caractérisation structurale de composés sous forme de poudre présente plus de difficulté. En particulier, beaucoup de composés ne peuvent pas être obtenus sous forme de monocristaux ; et les composés hautement polymorphiques (tels que la plupart des médicaments) doivent être caractérisés « tels quels » afin de limiter les risques de modification structurale. Cette thèse présente de nouvelles méthodes de cristallographie de poudre par résonance magnétique nucléaire (RMN) du solide à haute résolution, i. E. La détermination de la structure, en abondance isotopique naturelle, de composés en poudre par RMN. Dans une première partie, le cas complexe de la résolution des spectres proton est abordé. Les possibilités offertes par la dernière génération de sondes RMN sont explorées et de nouvelles méthodes de découplage sont proposées. Dans la deuxième partie, des protocoles de détermination structurale sont développés. Ces derniers s’appuient sur la forte dépendance des paramètres RMN avec les détails de la structure cristalline, et profitent de la haute résolution accessible en RMN du solide pour les protons et les carbones. Ces techniques sont appliquées à un composé test, le thymol, et démontrent le potentiel de la RMN du solide pour la résolution de la structure cristalline de composés en poudreKnowledge of the three-dimensional structure is an invaluable element for the understanding of the properties of solid materials and towards the development of new materials. While single-crystal X-ray diffraction is established as the best tool to characterise monocrystalline samples, the experimental determination of the structure of polycrystalline powders remains a challenging domain. Many crystalline solids cannot be prepared as single crystals and must be characterized in the powder form. Other compounds are highly subject to polymorphism, and there is a need for structural determination techniques that minimize the risk of structural change during the characterisation. The problem is particularly relevant in the case of drug powders, which need to be accurately characterized in their active pharmaceutical form. This thesis presents new developments relating to powder nuclear magnetic resonance (NMR) crystallography, i. E. Structure determination of powdered samples using high-resolution solid-state NMR at natural isotopic abundance. The first part of the thesis concentrates on the challenging case of protons and illustrates the opportunities offered by the latest generation of commercial NMR probes and new decoupling methods. Protocols are proposed in the second part, which benefit of the high-resolution solid-state NMR spectra accessible for protons and carbons and which make use of the strong dependence of the NMR parameters on crystalline structure details. These techniques are successfully applied to a model compound, thymol, and demonstrate the potential of solid-state NMR for structural determination of powdered compounds
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Özmen, Bahar Eanes Mehtap Thesis advisor. "Hydrothermal synthesis of solid state materials and crystallography/." [s.l.]: [s.n.], 2004. http://library.iyte.edu.tr/tezler/master/kimya/T000479.pdf.
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Geissbühler, Marc Phillip. "X-ray interfacial crystallography of water on calcite /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9634.
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Schenk, Andreas Daniel. "Structure determination of membrane proteins by electron crystallography /." Basel : [s.n.], 2007. http://edoc.unibas.ch/diss/DissB_7930.
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Lübben, Anna. "Algorithms for Crystal Structure Determination in Macromolecular Crystallography." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0005-12B9-6.
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Sadow, Jennifer Beth Hurley. "The X-ray crystal structure of wheat translation initiation factor eIF4E /." Thesis, Full text (PDF) from UMI/Dissertation Abstracts International, 2002. http://wwwlib.umi.com/cr/utexas/fullcit?p3085056.
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Magee, Iris. "Isometries in three space and the seven solid crystal systems." CSUSB ScholarWorks, 1995. https://scholarworks.lib.csusb.edu/etd-project/1110.
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Davies, Robert. "Methods development and radiation damage studies in macromolecular crystallography." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.491362.
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Radiation damage limits the amount of time that a macromolecular crystal diffracts when exposed to X-ray irradiation. Various aspects of this problem were inv~stigated in this work along with methods development for quantitative determination of the metal content of proteins and celIs. In particular, the iron storage protein ferritin was used to extend current understanding of the changes that occur in macromolecular crystals held at 100 K during exposure to X-rays. The characteristics of the expl!nsion in unit celI volume with absorbed dose and with temperature were examined and found to be distinguishable. A comparison between the iron loaded (holo) and the iron void (apo) forms of ferritin alIowed the contribution to the damage ofthe absorbing iron core to be determined. Glutaraldehyde cross-linking was also tested as a method to increase r~diation resistance. Experiments were carried out to establish the room temperature dose limit of protein crystals and compare this with the dose limit measured at cryotemperatures. Surprisingly, it was found that there was a significant decrease in radiation damage at higher dose rates. An online microspectrophotometer at the European Synchrotron Radiation Facility was used to screen large numbers of potential radioprotectants at 100 K by monitoring the absorbance spectra of the 400 nm peak associated with a disulphide radical anion formed by X-ray cleavage of a disulphide bond. Ascorbate, quinone, TEMP and DIT were identified as effective radioprotectants. The most promising radioprotectant (ascorbate) was put into co-crystallisation and soaking trials with lysozyme to measure its protective effect against X-ray induced damage at 100 K and room temperature. For high throughput trace element detection, XRF was investigated, but calibration for proteins proved problematic. MicroPIXE was used for trace element mapping of wild type and Niemann Pick TypeC (a neurodegenerative disorder) cells to identify alterations in trace element composition.
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Zwart, Petrus Hendrik. "Error estimation and pattern recognition techniques in protein crystallography." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2003. http://dare.uva.nl/document/68420.
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Christensen, Kirsten Elvira. "Open-Framework Germanates : Crystallography, structures and cluster building units." Doctoral thesis, Stockholm : Department of Physical, Inorganic and Structural Chemistry, Stockholm university, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7501.
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Collins, Anna. "The X-ray crystallography of Z'>1 materials." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437369.
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Lo, Victor Lai-Xin. "Iterative projection algorithms and applications in x-ray crystallography." Thesis, University of Canterbury. Electrical and Computer Engineering, 2011. http://hdl.handle.net/10092/5476.
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X-ray crystallography is a technique for determining the structure (positions of atoms in space) of molecules. It is a well developed technique, and is applied routinely to both small inorganic and large organic molecules. However, the determination of the structures of large biological molecules by x-ray crystallography can still be an experimentally and computationally expensive task. The data in an x-ray experiment are the amplitudes of the Fourier transform of the electron density in the crystalline specimen. The structure determination problem in x-ray crystallography is therefore identical to a phase retrieval problem in image reconstruction, for which iterative transform algorithms are a common solution method.
This thesis is concerned with iterative projection algorithms, a generalized and more powerful version of iterative transform algorithms, and their application to macromolecular x-ray crystallography. A detailed study is made of iterative projection algorithms, including their properties, convergence, and implementations. Two applications to macromolecular crystallography are then investigated. The first concerns reconstruction of binary image and the application of iterative projection algorithms to determining molecular envelopes from x-ray solvent contrast variation data. An effective method for determining molecular envelopes is developed. The second concerns the use of symmetry constraints and the application of iterative projection algorithms to ab initio determination of macromolecular structures from crystal diffraction data. The algorithm is tested on an icosahedral virus and a protein tetramer. The results indicate that ab initio phasing is feasible for structures containing 4-fold or 5-fold non-crystallographic symmetry using these algorithms if an estimate of the molecular envelope is available.
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Lees, Nicholas Sean. "EPR crystallography : studies of defect centres in single crystals." Thesis, University of Canterbury. Chemistry, 2001. http://hdl.handle.net/10092/6077.
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This thesis presents the results of precise X-band electron paramagnetic resonance studies of zircon (ZrSiO4) and α-quartz (SiO2) single crystals at temperatures between 15 and 100 K, and the synthesis of the zircon crystals studied.
Zircon crystals have been grown using the flux-growth technique, producing well-shaped crystals up to 4 mm in length. The technique was used to grow both doped and nominally undoped crystals. Dopants successfully incorporated into the zircon crystals were titanium, chromium, yttrium, aluminium and boron.
Analysis of Ti4+ /Y3+ -doped zircon crystals revealed four defect centres new to the Canterbury research group. Two oxygenic hole centres have been analysed, one compensated by yttrium ([SiO4/Y]0), and the other by an unknown ion ([SiO4/M]n). A crystal-field spin-orbit coupling analysis of hole centres with a range of g values has shown that their anisotropy may be directly related to crystal-field splittings of orbital energy levels. A Ti3+ electron centre, Si(Ti3+), has been shown to be located in a silicon lattice position in contrast to an earlier-discovered Ti3+ centre in a zirconium lattice position, Zr(Ti3+). Another electron centre labelled H (g∥ = 1.9875, g⊥ = 1.9550) has been measured,but is not yet understood.
A previously observed electron centre (Z) with effective g values of 1.9991 and 3.9118 has been shown to be a chromium ion in a silicon lattice position. A +3 oxidation state, and a large zero-field splitting has been inferred from an analysis of the effective g values. Two closely related boron centres have been observed in zircon crystals with relatively high boron doping, and have been interpreted as impurity electron centres in a zirconium lattice site. Both have almost identical g values gx = 1.969, gy = 1.981, gz = 1.969. One of the centres has the unusual point-group symmetry for defects in zircon of mm2 (C2v), which is explained by two adjacent ions along one of the zircon fourfold rotation-inversion axes.
Two centres in a-quartz have been measured and analysed. One has been interpreted as a silicon-vacancy oxygenic-hole centre, [HLi2O4]0, compensated by one hydrogen and two lithium ions. The hyperfine matrices have been analysed with some success using three different methods to ascertain the locations of the compensating nuclei. The second centre is a previously reported hydrogen-compensated iron centre in a silicon lattice site, [FeO4/H]0α. A pseudo cube analysis has been carried out in order to confirm the location of the iron ion, but the results have been found inconclusive.
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Alves-Areias, A. "Investigation of host-guest interactions by x-ray crystallography." Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395365.
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