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Chakroff, Aleksandr. "Discovering Structure in the Moral Domain." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467227.
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Early moral psychologists identified the moral domain with a class of actions that negatively impacted the wellbeing of others or violated their rights. However, anthropological work suggested that this view failed to capture the full extent of the moral domain, which can include victimless actions (e.g., food taboos), especially among socially conservative or non-Western individuals. Which kinds of acts are included in the moral domain? Along which dimensions do the acts differ from one another?
Paper 1 utilizes a data-driven approach to mapping the moral domain, revealing a simple two-factor structure that captures variance in moral judgments across individuals, as well as reliable cross-voxel pattern information within individual brains. The remaining papers investigate judgments of agents who perform “harmful” acts (e.g., assault) versus “impure” acts (e.g., incest), which are each representative of the separate factors discovered in Paper 1. In Paper 2, we see an asymmetry in people’s causal attributions for the actions of harmful versus impure agents: impure acts are judged as more internally generated, and less due to the situation, compared to harmful acts. This asymmetry is due to differences in abnormality, a key dimension along which the moral domain may be organized. Paper 3 probes agent evaluations: how are harmful and impure agents expected to act in other contexts? People expect harmful agents to be harmful but not impure. In contrast, people expect impure agents to be both impure and harmful. This effect is connected to a model of the moral domain with a conceptual “core” of dyadic harm, surrounded by a periphery of victimless moral violations. Together, this work highlights a simple structure in the moral domain that can explain moral judgments, causal attributions, action predictions, as well as patterns of activity in the cortex.Psychology
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Malbec, Aurélien. "Domain formation and evolution in ferroelectric materials." Thesis, Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/15905.
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Siddiqui, Nadeem. "Structure and function of the PABC domain." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=102727.
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The poly (A)-binding protein (PABP) is an essential protein found in all eukaryotes and functions in mRNA metabolic and translational processes. Structurally, PABP consists of two distinct regions. The N-terminal half contains four RNA recognition motifs that bind to the poly (A)-tail of mRNA, while the C-terminal segment contains a unique peptide binding module referred to as the PABC domain. The function of this domain in PABP is to recruit proteins containing a very specific 'PAM-2' motif to the mRNP complex. Unique to metazoans, a PABC domain is also found in the hyperplastic discs tumor suppressor (HYD), which is an E3 ubiquitin ligase.This thesis completes a structural investigation of PABC domains from various species by nuclear magnetic resonance spectroscopy. In particular, we report the solution structure of PABC from the parasite Trypanosoma cruzi and plant Triticum aevestium PABP. Both domains consist of five alpha-helices which fold into a structure highly comparable to the human PABC domain from PABP and HYD. All four PABCs interact with a similar PAM-2 sequence and show comparable peptide binding surfaces. The human PABC-PAM-2 complex structure displays a PAM-2 peptide interacting with specific residues within the domain. Sequence analyses and peptide surface mapping studies show that these residues are highly conserved, which indicates an analogous mechanism of peptide recognition throughout animal, parasite, and plant species. An exception to these observations was found in the PABC domain from Saccharomyces cerevisiae PABP. Yeast PABC recognizes a variation of the typical PAM-2 motif but mediates its interaction through a similar mechanism as human PABC.
The PAM-2 motif encloses a signature sequence which was used to successfully identify new interacting partners for the PABC domain via a bioinformatics screen. In mammalian systems, the identified proteins are implicated in either RNA metabolic, translational, or ubiquitin associated functions. This thesis concludes with a model illustrating a unique cross-talk between major gene expression pathways mediated by the PABC domain and its binding partners.
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McCabe, Veronica Mary. "Domain structure of the mouse Xist gene." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286333.
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de, Bono S. "Structure of an artificial chimaeric protein domain." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598444.
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This work describes the structure of an artificial chimaeric protein, 1B11, generated by non-homogeneous recombination between a defined gene fragment coding for the N-terminal half of E. coli cold shock protein (CspA), and a randomly selected C-terminal portion. The N-terminal segment of 1B11 consists of the first 36 residues of CspA, which forms three antiparallel beta strands. The termination point of this structural entity corresponds to a well conserved exon boundary in eukaryotic homologs of CspA. The C-terminal segment of 1B11 is derived fro the first 34 residues of the E. coli 30S ribosomal S1 domain. Both CspA and the S1 domain are monomeric globular proteins and have a five stranded beta barrel topology. 1B11 not only is tetrameric, but also has a different architecture, composed of a six-stranded beta barrel in which two strands are domain swapped. The individual segments taken from the original structures, have, however, retained much the same topology. The overall OB-fold topology is well maintained, with the first three strands of 1B11 being superimposable with those of CspA. Two strands from the C-terminal half of 1B11 have come to occupy spatially similar positions to the fourth and fifth strand of CspA. Also, hydrophobic residues in the 1B11 barrel core recapitulate barrel packing in the original structure. The sixth strand of 1B11 has been accommodated at the periphery of the barrel, such that a number of hydrophobic residues are solvent exposed. Oligomerisation in the form of tetramer formation and domain swapping allows stabilization of the structure by burying those hydrophobic residues. A combination of two non-contiguous subdomain elements has given rise to a folded domain with novel architecture and composition. This is consistent with the creation of domains by exon shuffling early on in evolution.
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Xu, Wenjing. "Crystal structure of paired domain--DNA complex." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32666.
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Bensaibi, Mahmoud. "Identification de la fonction de transfert d'une structure ou d'une sous-structure par méthodes fréquentielles et temporelles." Châtenay-Malabry, Ecole centrale de Paris, 1996. http://www.theses.fr/1996ECAP0468.
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Le présent mémoire comporte deux parties. La première partie approfondit la méthode d'identification ARMA appliquée aux structures. Une connaissance approfondie de cette technique est nécessaire si l'on veut être capable de régénérer de manière précise à partir d'une identification, les fonctions de transfert données par un analyseur. Pour cette raison nous avons mené une étude dans le domaine fréquentiel, afin d'avoir des élements de comparaison et une étude dans le domaine temporel, qui a nécessité des développements concernant la méthode ARMA. Un exemple expérimental a éte teste pour valider les techniques proposees dans les deux domaines temporel et frequentiel. En deuxieme partie, on a developpe tant en fréquentiel qu'en temporel une méthode d'identification de sous-structures in situ. Cette identification s'oppose au problème bien connu de synthèse modale. Au contraire de celle-ci, qui a pour but de reconstruire le comportement globale de la structure à partir de ses sous-structures, on cherche à partir du comportement global d'une structure, à identifier les caractéristiques dynamiques d'une sous-structure appartenant à cette structure totale. C'est donc un problème d'identification locale. Cette étude ayant pour objet une analyse expérimentale, le bruit de mesure est pris en considération. Des exemples numériques ont été présentés et ont montrés qu'on obtenait de bon resultats jusqu'à un niveau de bruit de 5% dans le domaine temporel et 2% dans le domaine frequentiel. Enfin, une validation expérimentale a été réalisée dont le but principal est de montrer l'efficacité de l'algorithme sur un cas réel. La régéneration de la fonction de transfert de la sous-structure à partir des paramètres identifiées est abordée également
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Hayashi, Masaki. "Studies of time-evolution of domain structure and domain interface structure in phase-separation process of two-component polymer systems." 京都大学 (Kyoto University), 2003. http://hdl.handle.net/2433/148838.
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Ramesh, Mahadevan. "Coupled oscillations of the magnetic domain-domain wall system in substituted garnet thin films /." The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487262513407393.
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Borcherds, Wade Michael. "Structure, Dynamics, and Evolution of the Intrinsically Disordered p53 Transactivation Domain." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4640.
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in numerous disease states, including cancers and neurodegenerative diseases. All proteins are dynamic in nature, occupying a range of conformational flexibilities. This inherent flexibility is required for their function, with ordered proteins and IDPs representing the least flexible, and most flexible, respectively. As such IDPs possess little to no stable tertiary or secondary structure, they instead form broad ensembles of heterogeneous structures, which fluctuate over multiple time scales. Although IDPs often lack stable secondary structure they can assume a more stable structure in the presence of their binding partners in a coupled folding binding reaction.
The phenomenon of the dynamic behavior of IDPs is believed to confer several functional advantages but remains poorly understood. To that end the dynamic and structural properties of a family of IDPs - p53 transactivation domains (TAD) was measured and compared with the sequence divergence. Interestingly we were able to find stronger correlations between the dynamic properties and the sequence divergence than between the structure and sequence, suggesting that the dynamic properties are the primary trait being
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conserved by evolution. These correlations were strongest within clusters of the IDPs that correlated with known protein binding sites. Additionally, we show strong correlations between the several available disorder predictors and the backbone dynamics of this family of IDPs. This indicates the potential of predicting the dynamic behavior of proteins, which may be beneficial in future drug design.
The limited number of atomic models currently determined for IDPs hampers understanding of how their amino acid sequences dictate the structural ensembles they adopt. The current dearth of atomic models for IDPs makes it difficult to test the following hypotheses:
1. The structural ensembles of IDPs are dictated by local interactions.
2. The structural ensembles of IDPs will be similar above a certain sequence identity threshold.
Based on the premise that sequence determines structure, structural ensembles were determined and compared for a set of homologous IDPs. Utilizing orthologues allows for the identification of important structural features and behaviors by virtue of their conservation. A new methodology of creating ensembles was implemented that broadly samples conformational space. This allowed us to find recurring local structural features within the structural ensembles even between the more distantly related homologues that were processed. This method of ensemble creation is also the first method to show convergence of secondary structural characteristics between discrete ensembles.
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Meissner, Torsten. "Structure-function analysis of the STAT1 N-domain." [S.l. : s.n.], 2005. http://www.diss.fu-berlin.de/2005/213/index.html.
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Murley, Laura Lea. "The domain structure of an octameric bifunctional enzyme." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40205.
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Formiminotetrahydrofolate:glutamate formiminotransferase (EC 2.1.2.5) - formiminotetrahydrofolate cyclodeaminase (EC 4.3.1.4) is a bifunctional enzyme arranged as a circular tetramer of dimers that exhibits the ability to efficiently channel polyglutamylated folate between catalytic sites. A novel, full-length cDNA clone encoding the porcine liver formiminotransferase-cyclodeaminase was isolated and inserted into a prokaryotic expression vector. The recombinant enzyme is expressed as a soluble protein in Escherichia coli and was purified to homogeneity using a multistep scheme. Deletion analysis of the cDNA indicated that each subunit consists of an N-terminal transferase-active domain and a C-terminal deaminase-active domain separated by a short linker sequence. These domains were expressed in Escherichia coli and demonstrated to exist as monofunctional dimers. This provides direct evidence for the existence of two types of subunit interfaces and suggests that both catalytic activities are dependent on the formation of specific subunit interfaces. Because channelling is not observed between isolated domains, only the octamer appears able to directly transfer pentaglutamylated intermediate between active sites. Thus we have established direct support for Findlay and MacKenzie's model (Findlay, W. A. & MacKenzie, R. E. (1987) Biochemistry 26, 1948-1954) that the octamer is the functional unit of the enzyme. The purified dimers show no tendency to associate, suggesting that the linker mediates the only substantial domain-domain interaction. The isolated domains and the full-length enzyme were subjected to urea-induced denaturation in order to characterize the properties of both domains in and outside of the octamer. At low concentrations of urea, both domains undergo a cooperative loss of fluorescence and activity, while maintaining their secondary structure and the majority of their quatenary structure. When the urea concentration is increased, coincident unfoldin
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Preston, Roger James Stephen. "The protein C Gla domain : structure-function relationships." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.416058.
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Zhang, Jian Jing. "Seismic soil-structure interaction in the time domain." Thesis, University of Canterbury. Civil Engineering, 2000. http://hdl.handle.net/10092/7849.
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A time domain analysis procedure and method for seismic soil-structure interaction analysis are introduced in this work. This includes the selection of the soil model, the far field model, the structural model and the soil-structure interaction analysis method.
The bounding surface plasticity model is implemented to model the near field. The boundary element method in the time domain is used as the far field model. A coupling method between the boundary elements and finite elements has been proposed, its main advantages being: equilibrium and compatibility conditions are used directly and the present boundary element and finite element packages only need a small modification before they are used in this coupled procedure.
Nonlinear local site analyses have been carried out. The comparisons of the effects of strong and weak input motions, different soft clay sites and different input motions on local site amplification show the effect of soil yielding on local site response.
A primary investigation of the effect of soil-structure interaction on structural response is carried out using the linear and nonlinear soil models. When the linear elastic model is used to represent the soil behaviour, the effects of different sites, frames and input motions from the basement rock on the soil-structure interaction are investigated. The results show that the natural vibration periods of the site and structure can represent the effect of the site and structure on the soil-structure interaction and the predominant period of the input motion can represent the effect of the input motion on soil-structure interaction. Acceleration response at the foundation, displacement at the top floor, inter-storey shear force and the rocking of the foundation are used to show the effect of the natural periods on the soil-structure interaction. When the nonlinear soil model is used to represent the soil behaviour, a comparison of the results of the linear and nonlinear analyses shows that the soil yielding has a great influence on vibration frequency and vibration amplitude of both the acceleration and the displacement at the foundation and at the top floor of the structures. The permanent settlement of the foundation shows its accumulative characteristics.
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Adawi, Hind. "Surface Effect Of Ferromagnetic Nanoparticles On Transition Between Single- And Multi-Domain Structure Or Between Single-Domain Structure And Superparamagnetic Phase." Wright State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=wright1484061850635516.
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Batra, Sharat. "Magneto-optical studies of domain wall oscillations /." The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487265555439935.
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Xu, Weiguang. "Solution structure of [Alpha]-syntrophin PH-PDZ tandem domain /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?BICH%202005%20XU.
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Li, Xuchu. "Crystal structure of the kelch domain of human keap1." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/5828.
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Thesis (Ph. D.)--University of Missouri-Columbia, 2005.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. Includes bibliographical references.
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Bran, Cristina. "Domain structure and magnetization processes of complex magnetic multilayers." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-33319.
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The magnetization processes of antiferromagnetically (AF) coupled Co/Pt multilayers on extended substrates and of Co/Pd multilayers deposited on arrays of 58 nm spheres are investigated via magnetic force microscopy at room temperature by imaging the domain configuration in magnetic fields. Adding AF exchange to such perpendicular anisotropy systems changes the typical energy balance that controls magnetic band domain formation, thus resulting in two competing reversal modes for the system. In the ferromagnetic (FM) dominated regime the magnetization forms FM band domains, vertically correlated. By applying a magnetic field, a transition from band to bubble domains is observed. In the AF-exchange dominated regime, by applying a field or varying the temperature it is possible to alter the magnetic correlation from horizontal (AF state) to vertical (FM state) via the formation of specific multidomain states, called metamagnetic domains. A theoretical model, developed for complex multilayers is applied to the experimentally studied multilayer architecture, showing a good agreement. Magnetic nanoparticles have attracted considerable interest in recent years due to possible applications in high density data storage technology. Requirements are a well defined and localized magnetic switching behavior and a large thermal stability in zero fields. The thermal stability of [Co/Pt]N multilayers with different numbers of repeats (N), deposited on nanospheres is studied by magnetic viscosity measurements. The magnetic activation volume, representing the effect of thermal activation on the switching process, is estimated. It is found that the activation volume is much smaller than the volume of the nanosphere and almost independent of the number of bilayers supporting an inhomogeneous magnetization reversal process.
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Lee, Wee Siang. "Exterior domain decomposition method for fluid-structure interaction problems." Thesis, Imperial College London, 1999. http://hdl.handle.net/10044/1/8533.
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Béve, Jenny. "Structure and function of the yeast mediator tail domain /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-599-2/.
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Gadhavi, Paresh Laxman. "The structure of the DNA-binding domain of GAL4." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240924.
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Williams, Samantha Catherine. "Studies of the domain structure of complement factor B." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358907.
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Gallagher, Thomas Robert Alexander. "The structure and dynamics of the p62-UBA domain." Thesis, University of Nottingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438269.
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Moores, Carolyn Ann. "Structure-function analysis of the utrophin actin binding domain." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624459.
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Bean, R. J. "Domain structure imaging by Bragg geometry X-ray ptychography." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1418466/.
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Domain structure in materials is important for their physical properties, technological uses and response to external perturbations. Domains are small regions within a material with a consistent atomic structure that may have different ordering origins or different orientations. Domain structure is present in any material which exhibits super-structure ordering with correlation lengths shorter than the extent of the sample. The domain size is controlled by the strength of the ordering interactions and growth conditions. Domains are present in a huge range of materials from con¬densed matter to biological samples with a structure unique to the individual sample. For domains in crystalline samples with sizes of Angstroms to nanometres X-rays are an ideal probe. Many domain systems exhibit no X-ray amplitude contrast, i.e. all domains attenuate the X-ray beam uniformly, the domain structure is apparent only in the deviation of the phase of the incident X-ray beam. An imaging method is required which is sensitive to these phase differences. Coherent X-ray Diffraction Imaging (CXDI) is a method which exploits the Fourier transform relationship between the sample and its far field diffraction pattern collected at a pixellated detector to iteratively solve the phase problem and reconstruct an amplitude and phase image of the sample. Support based coherent X-ray diffraction methods have been successfully applied to the three dimensional imaging of crystalline structures by collecting the scattering around the sample Bragg peaks in reflection geometry. In general, phase retrieval algorithm constraints require that the sample is isolated within the X-ray beam and as a result these methods have not been successful at imaging extended domain systems. Ptychography is a combined experimental and analysis procedure that can overcome the requirement for the sample to be isolated by collecting a series of diffraction patterns from overlapping regions of the sample. This thesis develops the ptychography algorithms and experimental methods for use in Bragg geometry with the goal of imaging phase domain structures in extended crystalline samples. Bragg coherent diffraction imaging and ptychography methods are reviewed before the adaptations of the experimental method and algorithm for the application of ptychography in Bragg geometry are discussed and detailed. Simulations of ptychography on phase domain structures and a Bragg geometry ptychography X-ray experiment with a specifically designed phase domain test sample confirm that the method is capable of providing accurate quantitative phase information on the domain structure of extended samples. A coherent diffraction experimental setup for ptychography is developed at Diamond beamline I16. Bragg ptychography is applied to the investigation of domain structure in a niobium thin film and anti-phase domain structure in the binary alloy Fe65Al35 and the results of the reconstructions are presented.
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Grimshaw, S. "The structure and interactions of the STE50 SAM domain." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599743.
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The MAPK cascade is a highly conserved signal transduction module that occurs throughout eukaryotic organisms. The control of the interactions between the various cascade components and their associated proteins is one level of control that exists to regulate the flow of information. The sterile alpha motif (SAM) was identified by searches for homologies between signal transduction proteins. Further database searches revealed that this 65-70 amino acid domain is found in approximately 70 proteins, whose function is involved in signal transduction or developmental regulation. SAM domains have been shown to mediate homo- and hetero-oligomerisation. For this report four SAM domains from the proteins STE50, STE11 (Saccharomyces cerevisiae), Ste4 and Byr2 (Schizosaccharomyces pombe) were cloned. All were expressed and purified successfully, and the solution structure of the STE50 SAM domain was determined. The homo- and heterotypic interactions of the STE50 SAM domain were also investigated using NMR, biophysical techniques such as analytical ultracentrifugation and dynamic light scattering, and by GST pull-down studies. Finally, residues important for the normal function of the STE50 SAM domain were identified by mutation.
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Geissinger, Jared Scott. "Structure-Function Analysis of the EsaR N-terminal Domain." Thesis, Virginia Tech, 2011. http://hdl.handle.net/10919/46190.
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The LuxR protein family is a class of quorum-sensing regulated bacterial transcription factors that alter gene expression as a function of ligand detection. This coincides with a high population density and/or a low rate of signal ligand diffusion. The majority of LuxR proteins are activated only in the presence of the signal ligand, an acyl-homoserine lactone (AHL). EsaR, from the corn pathogen Pantoea stewartii, represents a subset of LuxR homologues that are active in the absence of AHL and deactivated by its presence. The mechanism by which EsaR responds to AHL in a manner opposite to that of the majority of LuxR homologues remains elusive. Unlike the majority of LuxR homologues, which require AHL for purification, EsaR can be purified and biochemically investigated in the absence and presence of AHL. This work sought to answer questions regarding the structure-function relationship of the LuxR homologue, EsaR.
Fluorescence anisotropy was used to determine the relative DNA-binding affinity of wild type EsaR and three AHL-independent EsaR variants in the presence and absence of AHL. This enabled for quantitative analysis of the relative binding affinities of these AHL-independent variants for the EsaR binding site, the esa box. The results demonstrate that one AHL-independent EsaR variant has a slightly higher affinity for the esa box in the presence, rather than the absence of AHL. The affinity of the other two for the DNA is not impacted by AHL, potentially due to an inability to transduce the signal of ligand detection to the DNA binding domain.
Constructs containing only the EsaR N-terminal domain (NTD) were also developed. These constructs circumvented solubility issues associated with the full-length protein, allowing for additional biochemical analysis. It was determined that the EsaR NTD alone is sufficient for multimerization and ligand binding. Additionally, preliminary X-ray crystallography efforts have established some of the early parameters required to solve the crystal structure of the EsaR ligand binding domain in both the presence and absence of AHL. If pursued, these structures would be the first solved of a LuxR homologue ligand binding domain in both the presence and absence of the native AHL, potentially demonstrating the conformational change that occurs as a result of ligand binding. Collectively, these findings have established some of the groundwork required to resolve the question of what sort of conformational changes occur in EsaR as a result of ligand binding.Master of Science
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Veras, Lea. "NMDA Receptor Transmembrane Domain: Structure and Divalent Ion Selectivity." Research Showcase @ CMU, 2014. http://repository.cmu.edu/dissertations/1036.
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During a synaptic signal, NMDA receptors are the only ionotropic glutamate receptor subfamily that besides glutamate require glycine and membrane depolarization to allow ion permeation. The depolarization is necessary to release Mg2+ of the channel of NMDA receptors. Of the ions that permeate these ion channels, Ca2+ is of importance because it is essential for learning and memory. Furthermore, NMDA receptor dysfunction has been associated with several nervous system disorders, and thus understanding NMDA receptor functions and dysfunctions are relevant for rational drug design. The mechanisms by which NMDA receptors select Ca2+ for permeation over all other physiological ions, while binding Mg2+ and restricting other ions’ permeation, are not well understood. We hypothesize that the slightly different atomic properties of Mg2+ and Ca2+ result in different mechanisms for how each divalent ion moves across the channel. To create a more complete picture of the permeation mechanism and prove our hypothesis, we performed a multi-level computational chemistry approach. Our research methods consisted of three main steps. The first step was to perform quantum chemical and molecular dynamic calculations to quantitatively predict ion interactions with solvents that mimic the heterogeneous environment of the protein. The second step consisted of modeling, refining, and equilibrating a homology model of the NMDA receptor transmembrane domain. The final step consisted of using the equilibrated transmembrane domain NMDA receptor model to study the actual ionic environment in the protein and simulate the energy involved in the permeation process. For the first step, we found that the solvents mimic the behavior of the residues in the core of our NMDA receptor model because in both set of systems Ca2+ is more permissive than Mg2+ to exchange ligands. As the conclusions in second and third steps, we also observed that the aspargines in the NMDAR model provide the ideal cage environment, that functions like branches and capture the each divalent ion. Hence, an equilibrated TMD NMDAR model was built, the presence of each divalent ion in the protein was simulated, and the permeation mechanism was better understood.
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Hawick, Kenneth Arthur. "Domain growth in alloys." Thesis, University of Edinburgh, 1991. http://hdl.handle.net/1842/10605.
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This thesis describes Monte-Carlo computer simulations of binary alloys, with comparisons between small angle neutron scattering (SANS) data, and numerically integrated solutions to the Cahn-Hilliard-Cook (CHC) equation. Elementary theories for droplet growth are also compared with computer simulated data. Monte-Carlo dynamical algorithms are investigated in detail, with special regard for universal dynamical times. The computer simulated systems are Fourier transformed to yield partial structure functions which are compared with SANS data for the binary Iron-Chromium system. A relation between real time and simulation time is found. Cluster statistics are measured in the simulated systems, and compared to droplet formation in the Copper-Cobalt system. Some scattering data for the complex steel PE16 is also discussed. The characterisation of domain size and its growth with time are investigated, and scaling laws fitted to real and simulated data. The simple scaling law of Lifshitz and Slyozov is found to be inadequate, and corrections such as those suggested by Huse, are necessary. Scaling behaviour is studied for the low-concentration nucleation regime and the high-concentration spinodal-decomposition regime. The need for multi-scaling is also considered. The effect of noise and fluctuations in the simulations is considered in the MonteCarlo model, a cellular-automaton (CA) model and in the Cahn-Billiard-Cook equation. The Cook noise term in the CHC equation is found to be important for correct growth scaling properties.
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Hake, Michael James. "Spectroscopic Characterization of the Interaction of Nck Domains with the Epidermal Growth Factor Receptor Juxtamembrane Domain." Case Western Reserve University School of Graduate Studies / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=case1207340174.
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Mora, Araque Luis. "Port-Hamiltonian modeling of fluid-structure interactions in a longitudinal domain." Thesis, Bourgogne Franche-Comté, 2020. http://www.theses.fr/2020UBFCD058.
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L'interaction fluide-structure (FSI) est un problème multi-physique (avec plusieurs domaines physiques) qui étudie l'action réciproque entre une structure et un écoulement de fluide à travers une surface ou une interface de couplage. Mathématiquement, l'interaction fluide-structure est décrite par un ensemble d'équations différentielles et de conditions aux limites, obtenues par une formulation d'Euler-Lagrange et les équations de Navier-Stokes, qui appartiennent respectivement à la structure et aux domaines fluides. Le comportement de FSI peut être étudié à l'aide de solutions numériques utilisant des méthodes d'éléments finis ou de différences finies. Une alternative à Euler-Lagrange dans la modélisation des systèmes physiques à économie d'énergie est le cadre port-hamiltonien, dans lequel la dynamique du système est décrite par une fonction non négative représentant l'énergie totale stockée dans le système, appelée Hamiltonian H. Le port -Le cadre Hamiltonien permet la modélisation du transfert d'énergie entre systèmes de différents domaines physiques. Un exemple intéressant de FSI est le mécanisme de production vocale des cordes vocales, où le flux d'air intraglottal génère un cycle de vibration qui produit la phonation. Dans ce contexte, les modèles numériques des cordes vocales sont pertinents pour explorer les effets de certaines procédures thérapeutiques ou chirurgicales. Ces dernières années, on s’intéresse de plus en plus à l’étude du flux d’énergie dans la glotte pour l’analyse de la physiopathologie des troubles de la voix. L'étude de ce type de système multi-physique peut être étendue à d'autres systèmes FSI dans lesquels un fluide en mouvement dans un domaine longitudinal interagit avec un système mécanique en mouvement transversal. Dans cette thèse, un modèle évolutif en dimension finie pour les systèmes FSI sera développé. La division du problème fluide-structure en n sous-systèmes interconnectés décrits par des modèles de dimension finie constitue une alternative à la formulation traditionnelle à dimension infinie. De plus, l'utilisation du cadre port-hamiltonien pour décrire la dynamique permet une caractérisation adéquate du flux d'énergie dans le système. Le but de cette étude est donc de développer un modèle dimensionnel dimensionnel et évolutif, axé sur le flux d’énergie pour les systèmes à structure fluide dans un domaine longitudinal et s’appliquant aux plis vocauxFluid-structure interaction (FSI) is a multi-physics problem (with multiple physic domains) that study the reciprocal action between a structure and a fluid flow through a coupling surface or interface. Mathematically, Fluid-structure interaction is described by a set of differential equations and boundary conditions, obtained by an Euler-Lagrange formulation and the Navier-Stokes equations, which belong to the structure an fluid domains respectively. The behavior of FSI can be studied through numerical solutions using finite elements or finite differences methods. An alternative to Euler-Lagrange in the modeling of the energy-conserving physical systems is the port-Hamiltonian framework where the system dynamics are described through a non-negative function that represents the total stored energy in the system, called Hamiltonian H. The port-Hamiltonian framework allows the modeling of the energy transfer between systems in different physical domains. An interesting example of a FSI is the voice production mechanism of the vocal folds, where the intraglottal airflow generates a vibration cycle that produces the phonation. In this context, numerical models of the vocal folds are relevant to explore the effects of certain therapeutic or surgical procedures. In recent years there has been a growing interest in the study of energy flux in the glottis for analysis of pathophysiology of vocal disorders. The study of this kind of multi-physics system can be extended to other FSI system where a fluid moving in a longitudinal domain interacts with a mechanical system that move in the transversal dimension. In this thesis, a scalable finite-dimensional model for FSI systems will be developed. The division of fluid-structure problem into n interconnected sub-systems described by finite-dimensional models, provide an alternative to the traditional infinite-dimensional formulation. In addition, the use of port-Hamiltonian framework to describe the dynamics allows an adequate characterization of the energy flux in the system. Thus, the aim of this study develop a scalable finite-dimensional model focused in the energy flux for fluid-structure systems in a longitudinal domain with application to vocal folds
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Zhao, Xiaofang, and 赵晓芳. "The influence of defects on the domain structure and properties of ferroelectrics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47031608.
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Al, Baqui Abeera Farzana. "Value-focused GAI network structure elicitation given a domain Ontology." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31542.
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Making optimal decisions is important yet challenging. A decision maker has to take into
account her preferences when she needs to make decisions. Often such preferences are over
features in the world and exhibit certain structure. It is possible to exploit this structure by
making assumptions of independence, to acquire a decision maker's preferences. However, a
compromise must be observed while making these assumptions -too many independence
assumptions means the preference model acquired is likely to be inaccurate, however too few
assumptions yields an overly complex model. A Generalized Additive Independence (GAI)
Network establishes a good compromise between the accuracy and the generality of the model.
A GAI network represents a decision maker's preferences in terms of its structure and a set of
utilities. Decision theory provides methods of obtaining both the structure and the utilities of a
GAI network; however, these methods are too time consuming, error prone and therefore
impractical. Several researchers have investigated methods for simplifying the elicitation
procedures for GAI network utilities. However, elicitation of a GAI network structure has not
received much attention. Value Focused Thinking (VFT) could be a promising solution to this
problem, as it can be used to reduce the number of elicitations required to build a DM's GAI
network structure as opposed to traditional decision theoretic methods such as standard
gambles.
VFT proposes that decision-making should start by decomposing a decision maker's values into
additively independent objectives (these are the fundamental objectives). VFT shows how to
acquire a decision maker's objectives and map attributes of a domain onto these objectives. We
assume that the attributes of a domain are represented in an ontology (which specifies the
vocabulary to describe the domain). The decision maker can specify how these attributes fulfill
their fundamental objectives.
It is tempting to build a system where non-expert decision makers, minimally trained in
concepts of VFT, Ontologies and GAI networks, may express their preferences by 1) specifying
objectives and 2) indicating attributes that fulfill these objectives thus creating a value tree.
Once a decision maker's value tree is elicited, it is possible to build a corresponding GAI
network.
However, it is required that the structure of a decision maker's value tree adhere to the
independence assumptions made for GAI networks. We set up an experiment to test whether
the structure obtained from eliciting a decision maker's value tree in this manner follows GAI
network independence assumptions. We tested this hypothesis in the real-estate domain and
found that the resulting structure does not reflect the independence assumptions of a GAI
network. We conclude by discussing implications and suggest changes to our original approach.Science, Faculty of
Computer Science, Department of
Graduate
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Stie, Jamal Talal. "Modulation of the Plasma Membrane Domain Structure of Human Neutrophils." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/stie/StieJ0806.pdf.
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Eukaryotic cell plasma membranes form an interface between cells and their environment and function to detect and interpret environmental cues. The work described in this dissertation examines the changes that occur in membrane structure during plasma membrane function in human neutrophils and a fungal opportunist. The body of this work examines how circulating neutrophils can remain functionally inactive in the presence of perturbing influences inherent in the blood circulation, and yet rapidly activate upon exposure to proinflammatory agents. It is hypothesized that the regulated modulation of plasma membrane domain structure determines the activation of blood-leukocytes, in vivo. Experimentation is based the isolation of blood-neutrophils in either nonactivated or activated (primed) cellular states using dextran- or gelatin-based preparative methods, respectively. Analysis of plasma membrane cortical components actin, fodrin, ezrin, CD45 and CD43 by sucrose density sedimentation, flow cytometry and indirect immunofluorescence microscopy indicated significant differences in the plasma membrane structure of both neutrophil populations. In nonactivated neutrophils, cortical actin and fodrin were cytosolic, thus indicating the absence of cortical structure in this population. However, cortical actin and fodrin were membrane-associated in activated neutrophils showing the existence of a cortex. Fodrin, actin, ezrin and their respective anchors, CD45 and CD43 did not codistribute with the plasma membrane marker, alkaline phosphatase, in sucrose density gradients made with primed neutrophils. These latter results suggested the lateral compartmentalization of the plasma membrane cortex into compositionally distinct surface domains. Additional studies were performed to examine the surface-association of hCap, a soluble microbicidal component of neutrophil specific granules. Results indicated association of hCap with primed and degranulated but not nonactivated plasma membranes. This interaction was resistant to 1M salt but labile to 10 mM NaOH, indicating a high affinity association. In support of this, hCap also co-partitioned with detergent in Triton X-114 phase experiments. In separate studies, marked alterations in the plasma membrane lipid metabolism of isolates from Candida glabrata are correlated with an ability to survive and grow in vivo. Altogether, this work provides insight into structure-function relationships at the plasma membrane level.
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Luczynski, Maciej Tomasz. "Structure-guided functional analysis of the pRb N-terminal domain." Thesis, University of London, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531336.
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Cowburn, R. P. "Magnetic switching and domain structure in ultrathin epitaxial magnetic films." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598084.
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A detailed experimental study using magnetooptics has been performed into magnetic switching and domain structure predominantly in high quality ultrathin epitaxial Ag/Fe/Ag(001) films, for both in-plane and out of plane magnetisation. When the magnetisation is in-plane, magnetic switching has been found to proceed by a series of irreversible jumps of the magnetisation direction, each of which is mediated by the sweeping of domain walls. A simple phenomenological model has been developed which explains the switching and which highlights the role of magnetic anistropy and domain wall pinning by defects. Further micromagnetic modelling, combined with experiments, showed that the defects which determine coercivity are atomic steps on the Fe surface (named 'micropins'). A series of time resolved studies revealed that in addition to the micropins there also exists a second domain wall pinning mechanism, named 'macropinning' which is due to extrinsic defects such as scratches and other surface damage and which is not primarily responsible for coercivity. It has been found possible to engineer artificially the magnetic properties of a Permalloy film by introducing controlled macropins through lithographic structuring. The interplay between dipolar effects and intrinsic anisotropy leads to a novel domain structure during switching which could have important technological applications. In contrast to the in-plane magnetised case, in which the domain structure is an interim state which mediates the magnetic switching, the out of plane magnetised system was found to adopt a domain structure as its preferred ground state for certain temperatures and film thicknesses. These have been described by a magnetic phase diagram.
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Raggett, Elaine. "The structure and function of translocation domain of Colicin N." Thesis, University of Newcastle Upon Tyne, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285400.
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Wang, Yongxing. "A one-field fictitious domain method for fluid-structure interactions." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/21218/.
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We present a one-field fictitious domain method (FDM) for simulation of general fluid-structure interactions (FSI). "One-field" means only one velocity field is solved in the whole (fluid and solid) domain based upon the finite element interpolation. The proposed method has the same generality and robustness as the FDM with a distributed Lagrange multiplier (DLM): both of them solve the fluid equations and solid equations as one system. However the one-field FDM only needs to solve for one velocity field while the FDM/DLM usually solves for fluid velocity, solid displacement and Lagrange multiplier. The proposed one-field FDM also has similar features with immersed finite element methods (IFEM): the explicit or implicit IFEM places all the solid information in a FSI force term which is arranged on the right-hand side of the fluid equations. The one-field FDM assembles the solid equations and implicitly includes them with the fluid equations. What we achieve is theoretically equivalent to an implicit IFEM but avoiding convergence problems, and a wide range of solid parameters can be considered in this scheme. In short, the one-field FDM combines the FDM/DLM advantage of robustness and the IFEM advantage of efficiency. In this thesis, we present a thorough review, summary and categorization of the existing finite element methods for FSI problems. The finite element weak formulation of the one-field FDM and discretization in time and space are introduced, followed by a stability analysis by energy estimate. The proposed scheme is first implemented in implicit form, followed by numerical validation for the property of non-increasing energy under the conditions of $\rho^f\le\rho^s$ (densities of the fluid and solid respectively) and $\nu^f\le\nu^s$ (viscosities of the fluid and solid respectively), and numerical tests for stability under the conditions of $\rho^f>\rho^s$ and/or $\nu^f>\nu^s$. The proposed scheme is then implemented based upon three explicit splitting schemes: 2-step splitting, 3-step splitting and 4-step splitting scheme. The fully coupled implicit FSI system is decoupled into subproblems step by step, which can be effectively solved. The pros and cons of these splitting schemes are analysed followed by a selection of numerical tests in order to illustrate the capabilities and range of applicability of the proposed one-field FDM scheme. The thesis concludes with a presentation of some topics and open problems that may be worthy of further investigation.
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Casal, Eva. "Structure and interactions of the Bin1/Amphiphysin II BAR domain." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614135.
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Li, Hongyuan. "Structure of KI67 FHA domain and its binding to HNIFK." The Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=osu1060882032.
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Yavari, Arash Ortiz Michael. "Atomic structure of ferroelectric domain walls, free surfaces and steps /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-12142004-121255.
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Rupert, Peter Benjamin. "Structure determination of the SKN-1 DNA binding domain complex /." view abstract or download file of text, 1999. http://wwwlib.umi.com/cr/uoregon/fullcit?p9947981.
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Thesis (Ph. D.)--University of Oregon, 1999.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 96-106). Also available for download via the World Wide Web; free to University of Oregon users. Address: http://wwwlib.umi.com/cr/uoregon/fullcit?p9947981.
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Zheng, LiangKan 1972. "Fluid-structure coupling for aeroelastic computations in the time domain using low fidelity structural models." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=99127.
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Flutter analysis plays an important role in the design and development of aircraft wings because of the information it provides regarding the flight envelope of the aircraft. With the coupling of the flow and structural solver, the flutter boundary of wings can be evaluated in the time domain. This study: First, computes the aeroelastic response for a typical sweptback wing section model by coupling a flow solver and a two degree of freedom structural equation of motion solver to predict the flutter boundary of an airfoil at different Mach numbers. The results agree well with previous numerical results, and the transonic-dip phenomenon can be observed. Second, a new coupling approach is introduced to conservatively transfer the load and displacement between the flow solver and the structural solver for 3-D flow. By coupling the flow solver and a low fidelity finite element structural model, the flutter point of AGARD wing 445.6 at Mach number 0.499 is computed. The flutter point agrees well with experimental results and previous numerical results.
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Sykes, Paul A. "Structure-property relationships of chain-extended thermoplastic polyurethane elastomers." Thesis, Loughborough University, 1999. https://dspace.lboro.ac.uk/2134/12451.
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The effect of chain extender chemical structure on the physical and mechanical properties of thermoplastic polyurethane/urethaneurea elastomers was systematically investigated. Several series of materials were synthesised using 4,4' -diphenylmethane diisocyanate (MDI) and poly(tetramethylene oxide) glycol (PTMG), each series incorporating a particular class of chain extender compound. Elucidation of the influence of chain extender structural variations within each series was the principal objective of the investigation…
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Hong, Liang, and 洪亮. "On nanoferroelectric domain structures and distributions of defects inferroelectrics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44138763.
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Wang, Yanchao. "Protein Structure Data Management System." Digital Archive @ GSU, 2007. http://digitalarchive.gsu.edu/cs_diss/20.
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With advancement in the development of the new laboratory instruments and experimental techniques, the protein data has an explosive increasing rate. Therefore how to efficiently store, retrieve and modify protein data is becoming a challenging issue that most biological scientists have to face and solve. Traditional data models such as relational database lack of support for complex data types, which is a big issue for protein data application. Hence many scientists switch to the object-oriented databases since object-oriented nature of life science data perfectly matches the architecture of object-oriented databases, but there are still a lot of problems that need to be solved in order to apply OODB methodologies to manage protein data. One major problem is that the general-purpose OODBs do not have any built-in data types for biological research and built-in biological domain-specific functional operations. In this dissertation, we present an application system with built-in data types and built-in biological domain-specific functional operations that extends the Object-Oriented Database (OODB) system by adding domain-specific additional layers Protein-QL, Protein Algebra Architecture and Protein-OODB above OODB to manage protein structure data. This system is composed of three parts: 1) Client API to provide easy usage for different users. 2) Middleware including Protein-QL, Protein Algebra Architecture and Protein-OODB is designed to implement protein domain specific query language and optimize the complex queries, also it capsulates the details of the implementation such that users can easily understand and master Protein-QL. 3) Data Storage is used to store our protein data. This system is for protein domain, but it can be easily extended into other biological domains to build a bio-OODBMS. In this system, protein, primary, secondary, and tertiary structures are defined as internal data types to simplify the queries in Protein-QL such that the domain scientists can easily master the query language and formulate data requests, and EyeDB is used as the underlying OODB to communicate with Protein-OODB. In addition, protein data is usually stored as PDB format and PDB format is old, ambiguous, and inadequate, therefore, PDB data curation will be discussed in detail in the dissertation.
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Christie, Laura Mary. "Domain processes of four magnetic thin film systems." Thesis, University of Glasgow, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.300660.
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Tilborg, Marc van. "The glucocorticoid receptor DNA binding domain : structure and allosteric modulation = het DNA binded domein van de glucocorticoide receptor /." [S.l. : s.n.], 1998. http://www.gbv.de/dms/bs/toc/250860244.pdf.
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Nassor, Alice. "Domain decomposition method for acoustic-elastic coupled problems in time-domain. Application to underwater explosions." Electronic Thesis or Diss., Institut polytechnique de Paris, 2023. http://www.theses.fr/2023IPPAE015.
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Ce travail étudie les approches globales en temps de décomposition de domaine pour résoudre des problèmes transitoires d'interaction fluide-structure. Afin de déterminer un algorithme optimal, nous étudions dans un premier temps la solvabilité des problèmes élastodynamiques et acoustiques transitoires avec des conditions aux frontières de type Robin et de Neumann. Nous énonçons des résultats de solvabilité, en soulignant les différentes régularités espace-temps des solutions. Nous étudions également la solvabilité du problème couplé élastodynamique-acoustique transitoire. Puis en nous basant sur ces résultats mathématiques, nous proposons ensuite un algorithme itératif global en temps basé sur les conditions aux limites de type Robin pour le problème couplé et prouvons sa convergence.Ces résultats sont ensuite mis en oeuvre pour coupler deux méthodes numériques efficaces. La réponse du fluide en temps discret est obtenue à l'aide d'une approche Z-BEM qui combine (i) une méthode d'éléments de frontière (BEM) accélérée par la méthode des matrices hiérarchiques dans le domaine de Laplace et (ii) une quadrature de convolution. La réponse de la structure est modélisée à l'aide de la méthode des éléments finis. Nous développons de cette manière une méthode numérique de couplage itérative globale en temps à convergence garantie, permettant en outre d'utiliser deux méthodes numériques distinctes de manière non intrusive.Plusieurs améliorations sont ensuite proposées: une méthode d'accélération de convergence est mise en œuvre et une approximation à haute fréquence est proposée pour améliorer l'efficacité de la Z-BEM. On propose ensuite un deuxième couplage itératif global-en-temps basé sur une interface acoustique-acoustique, dont la convergence est également démontrée. Ce couplage permet ensuite d'introduire des effets non linéaires dus au phénomène de cavitation pour préciser le modèle fluide. La Z-BEM est enfin adaptée en utilisant la méthode des images pour permettre la prise en compte d'une surface libre.Cette méthode est appliquées à des problèmes à dynamique rapide de dispersion d'ondes de choc acoustiques par des structures élastiques immergées et permet de simuler des configurations réalistes rencontrées dans l'industrie navaleThis work addresses global-in-time domain decomposition approaches for the numerical solution of transient fluid-structure interaction problems. To determine an optimal algorithm, we first study the solvability for the transient acoustic and elastodynamic problems with Robin and Neumann boundary conditions. We state solvability results along with the different space-time regularities of the solutions. We also study the solvability for the transient coupled elastodynamic-acoustic problem. Using on these mathematical results we then propose a global-in-time iterative algorithm based on Robin boundary conditions for the coupled elastodynamicacoustic problem and we prove its convergence.These results are leveraged to design a computational methodology by coupling two efficient numerical methods. The fluid response is formulated in the discrete-time domain, using a Z-BEM approach that combines (i) a boundary element method (BEM) accelerated with hierarchical matrix implemented in the Laplace domain and (ii) a convolution quadrature method. The structure response is modelled using the finite elements method. We thus propose a global-in-time iterative coupling with guaranteed convergence, which enables the use of two distinct numerical methods in a non-intrusive manner.Several improvements are then explored: an acceleration method is implemented and a high-frequency approximation is proposed to improved the Z-BEM efficiency. A second iterative global-in-time coupling based on an acoustic-acoustic interface is then proposed and its convergence is also proved. This coupling enables the addition of non linear effects due to the cavitation phenomenon to derive a more realistic fluid model. The Z-BEM is lastly adapted using the method of images to take a free surface into account.This method is applied on fast-time problems of acoustic shock wave scattering by submerged elastic structures and enables to simulate realistic configurations from naval industry