Dissertations / Theses on the topic 'Nuclei anisotropici'

Lo scopo della presente tesi è quello di discutere i risultati ottenuti durante i miei studi di dottorato, principalmente rivolti a problemi non locali. Per prima cosa ci occupiamo di principi di continuazione unica forte ed espansioni asintotiche locali in determinati punti del bordo per soluzioni di due diverse classi di equazioni ellittiche. In particolare, partiamo con lo studio di una classe di equazioni ellittiche frazionarie in un dominio limitato sotto una condizione al contorno di Dirichlet omogenea esterna. Per fare ciò, sfruttiamo la procedura di estensione di Caffarelli-Silvestre, grazie alla quale il problema non locale può essere riformulato in modo equivalente come problema locale in una dimensione in più, generando un problema con condizioni miste. Dopodichè, utilizziamo un'idea classica di Garofalo e Lin per ottenere una condizione di raddoppio tramite una formula di monotonia per la funzione di Almgren. Per superare le difficoltà legate alla perdita di regolarità in corrispondenza della transizione tra le regioni di Dirichlet e di Neumann, introduciamo una nuova tecnica basata su un argomento di approssimazione, che ci permette di derivare una cosiddetta identità di tipo Pohozaev necessaria per stimare la derivata della funzione di Almgren . Otteniamo così un risultato di continuazione unica forte nel contesto locale, che viene a sua volta combinato con l’analisi di blow-up per dedurre espansioni asintotiche locali e, di conseguenza, una continuazione unica forte anche nel contesto non locale. Inoltre forniamo anche un risultato di continuazione unica forte dal bordo di una fessura per le soluzioni di una classe specifica di equazioni ellittiche del secondo ordine in un dominio limitato aperto con una frattura, su cui è assegnata una condizione al contorno di Dirichlet omogenea. Questo problema locale è correlato a un caso particolare dello studio descritto sopra, in virtù di una forte connessione tra questo tipo di problemi e i problemi al contorno con condizioni miste. Nella presente dissertazione, trattiamo anche una teoria della capillarità non locale. In particolare, consideriamo nuclei di interazione più generali che sono possibilmente anisotropici e non necessariamente invarianti rispetto allo stesso riscalamento. In particolare, la perdita di invarianza è modellata utilizzando due diversi esponenti frazionari per tenere conto della possibilità che il contenitore e l'ambiente presentino caratteristiche diverse rispetto alle interazioni delle particelle. Determiniamo inoltre una legge di Young non locale per l'angolo di contatto tra la gocciolina e la superficie del contenitore e discutiamo la solvibilità e l’unicità della soluzione dell'equazione corrispondente in termini di nuclei di interazione e del relativo coefficiente di adesione.
The aim of the present thesis is to discuss the results obtained during my PhD studies, mainly devoted to nonlocal issues. We first deal with strong unique continuation principles and local asymptotic expansions at certain boundary points for solutions of two different classes of elliptic equations. We start the investigation by a class of fractional elliptic equations in a bounded domain under some outer homogeneous Dirichlet boundary condition. To do this, we exploit the Caffarelli-Silvestre extension procedure, which allows us to get an equivalent formulation of the nonlocal problem as a local problem in one dimension more, consisting in a mixed Dirichlet-Neumann boundary value problem. Then, we use a classical idea by Garofalo and Lin to obtain a doubling-type condition via a monotonicity formula for a suitable Almgren-type frequency function. To overcome the difficulties related to the lack of regularity at the Dirichlet-Neumann junction, we introduce a new technique based on an approximation argument, which leads us to derive a so-called Pohozaev-type identity needed to estimate the derivative of the Almgren function. Thus we gain a strong unique continuation result in the local context, which is in turn combined with blow-up arguments to deduce local asymptotics and, consequently, a strong unique continuation result in the nonlocal setting as well. We also provide a strong unique continuation result from the edge of a crack for the solutions to a specific class of second order elliptic equations in an open bounded domain with a fracture, on which a homogeneous Dirichlet boundary condition is prescribed, in the presence of potentials satisfying either a negligibility condition with respect to the inverse-square weight or some suitable integrability properties. This local problem is related to a particular case of the setting described above, by virtue of a strong connection between this type of problems and the mixed Dirichlet-Neumann boundary value problems. We also treat a capillarity theory of nonlocal type. In our setting, we consider more general interaction kernels that are possibly anisotropic and not necessarily invariant under scaling. In particular, the lack of scale invariance is modeled via two different fractional exponents in order to take into account the possibility that the container and the environment present different features with respect to particle interactions. We determine a nonlocal Young's law for the contact angle between the droplet and the surface of the container and discuss the unique solvability of the corresponding equation in terms of the interaction kernels and of the relative adhesion coefficient.

Physical forces in the cellular microenvironment play an important role in governing cell function. Forces transmitted through the cell cause distinct deformation of the nucleus, and possibly play a role in force-mediated gene expression. The work presented in this thesis drew upon innovative strategies employing simultaneous atomic force and laser-scanning confocal microscopy, as well as parallel optical stretching experiments, to gain unique insights into the response of eukaryotic cell nuclei to external force. Non-destructive approaches confirmed the existence of a clear anisotropy in nuclear mechanical properties, and showed that the nucleus' mechanical response to extracellular forces is differentially governed by both nuclear and cytoskeletal prestress: nuclear prestress regulates shape and anisotropic deformation, whereas cytoskeletal prestress modulates the magnitude and degree of deformation. Importantly, the anisotropic mechanical response was conserved among diverse differentiated cell types from multiple species, suggesting that nuclear mechanical anisotropy plays an important role in cell function.

The angular dependence of the differential scattering cross section is typically represented as a truncated Legendre series expansion. If the scattering cross section is highly anisotropic, these expansions may result in negative regions in the -1 ≤ μ0 ≤ +1 interval, thus representing the cross section by negative values. These negative regions may cause negative components in the discrete ordinates scattering source, which are non-physical and which may adversely affect the iterative convergence of the exponential discontinuous spatial discretization scheme. Two methods are presented which produce a positive representation of the scattering cross section, and are designed to calculate a strictly positive scattering source. The first method constructs a scattering matrix from the exponential representation of the cross section derived from maximum entropy. Accuracy of these matrices is further improved by the application of SMART scattering theory. The second method adjusts the Legendre cross section moments with a constrained least squares algorithm. The adjustment is subject to constraints that the zeroth and first moment remain unchanged and that the resulting expansion is positive on all scattering angle cosines derived from a standard S N quadrature set. Extra moments from the maximum entropy representation of the cross section are also used to decrease the relative error of the modified moments. Numerical transport calculations using these two methods demonstrate consistent results with those using the standard truncated Legendre expansion of the cross section. The exponential discontinuous spatial scheme is shown to iteratively converged when these two methods are used. A comparison of these methods with results from multigroup and continuous energy Monte Carlo calculations are also shown to be consistent.

The linear Boltzmann equation for the transport of neutral particles is investigated with the objective of generating benchmark-quality calculations for homogeneous infinite media. In all cases, the problems are stationary, of one energy group, and the scattering is both isotropic and anisotropic. In the transport problems considered, the Green's function is generally the quantity of interest. The solution is obtained through the use of the Fourier transform method. The numerical inversions use standard numerical techniques, such as Gauss-Legendre quadrature, summation of infinite series, and Euler-Knopp acceleration. The most basic source of neutral particles is the point-beam source, or Green's function source. The Green's function in an infinite medium with isotropic scattering is treated as explained in chapter two. The Green's function in an infinite medium with anisotropic scattering is treated using two different mathematical methods as explained in chapters three and four. The results for both cases is shown in chapter 5.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 81-85).
Coherent control is a fundamental challenge in quantum information processing (QIP). Our system of interest employs a local, isolated electron spin to coherently control nuclear spins. Coupled electron/nuclear spins are a promising candidate for QIP: nuclear spins are used for information storage and computation due to their long coherence times, while the electron is used as a spin actuator for initialization, information transfer, control, and readout. This is the first implementation of a local processor using the central qubit architecture. In this work, a robust integrated system for coherent control of these spins is proposed. The system includes a mechanical and cryogenic system for sample handling, cooling, and suspension; computer software for experimental control and optimal control pulse determination; and a custom-designed pulsed electron spin resonance (ESR) spectrometer with digital signal acquisition and processing. The spectrometer enhances and expands past contributions of J. S. Hodges and J. C. Yang, who built a first generation device capable of amplitude modulated control pulses. The new device features improved noise properties, higher power, better carrier and sideband rejection, and a more customizable analysis via digital signal processing. It also implements both amplitude and phase modulation of control pulses. Further, it introduces the ability to address different resonances in the spin system by switching intermediate frequencies while maintaining phase coherence. Our work concludes with a signal-to-noise ratio (SNR) analysis that demonstrates improvement of more than a factor of 15 compared to the earlier device.
by Mohamed Osama Abutaleb.
S.M.

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências Físicas e Matemáticas, Programa de Pós-Graduação em Física, Florianópolis, 2014.
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Neste trabalho estudamos o comportamento da magnetização de um sistema de nanopartículas magnéticas não interagentes, monodomínio, com anisotropia uniaxial. Foram realizadas simulações de Monte Carlo através do algoritmo de Metropolis para analisar a relaxação magnética das nanopartículas inicialmente magnetizadas à saturação, na ausência e na presença de um campo magnético externo. A lei de escala Tln(t) foi utilizada para computar os dados da relaxação em diferentes temperaturas, gerando uma única curva mestra para cada valor de campo aplicado. Através dessas curvas podemos obter as distribuições das barreiras de energia do sistema e verificar a influência do campo externo na inversão da magnetização.

Abstract : In this work the behavior of the magnetization of a system composed by noninteracting magnetic nanoparticles, monodomains, with uniaxial anisotropy is studied. Monte Carlo simulations were performed through the Metropolis algorithm to analyse the magnetic relaxation when, at the beginning of the experiment, all the nanoparticles are magnetized to saturation, in the presence or absence of an external magnetic field. The scaling law Tln(t) was used to compute the relaxation data for different temperatures providing one master curve for each value of the applied field. From these curves we find the energy barriers distribution of the system and we verify the effect of the magnetic field on magnetization reversal.

Ultra-Relativistic heavy-ion physics is a promising field of high energy physics connecting two fields: nuclear physics and elementary particle physics. Experimental achievements of the last years have provided an opportunity to study the properties of a new state of matter created in heavy-ion collisions called quark-gluon plasma. The initial state of two colliding nuclei is affected by fluctuations coming from wave- functions of nucleons. These fluctuations lead to the momentum anisotropy of the hadronic matter which is observed by the detectors. The system created in the collision behaves like a fluid, so the initial state is connected to the final state via hydrodynamic evolution. In this thesis we model the evolution with relativistic viscous hydrodynamics. Our results, combined with experimental data, give non trivial constraints on the initial state, thus achieving "reverse engineering" of the heavy-ion collisions. The observable which characterizes the momentum anisotropy is the anisotropic flow vn. We present the first measurements of the first harmonic of the anisotropic flow called directed flow v1 in Pb-Pb collisions at the LHC. We then perform the first viscous hydrodynamic modeling of directed flow and show that it is less sensitive to viscosity than higher harmonics. Comparison of these experimental data with the modeling allows to extract the values of the dipole asymmetry of the initial state, which provides constraints on the models of initial states. A prediction for directed flow v1 in Au-Au collisions is also made for RHIC. We then perform a similar modeling of the second and third harmonics of the anisotropic flow, called respectively elliptic v2 and triangular v3 flow. A combined analysis of the elliptic and triangular flow data compared with viscous hydrodynamic calculations allows us to put constraints on initial ellipticity and triangularity of the system. These constraints are then used as a filter for different models of initial state. At the end of this thesis, we show perspectives in the studies of the initial state which are opened by recent measurements of event-plane correlations which could shed light on the initial state fluctuations.

Sedimentary rocks are characterized with very low permeability (in the order of 10-22 m2), low diffusivity, a possible self-healing of fractures, and a good capacity to retard radionuclide transport. In recent years, sedimentary rocks are investigated by many research groups for their suitability for the disposal of radioactive waste. Development of deep geologic repositories (DGRs) for the storage of radioactive waste within these formations causes progressive modification to the state of stress, to the groundwater regime, and to the chemistry of the rock mass. Thermal effects due to the ongoing nuclear activity can cause additional disturbances to the system. All these changes in the system are coupled and time-dependent processes. These coupled processes can result in the development of an excavation damaged zone (EDZ) around excavations. More permeable than the undisturbed rock, the EDZ is likely to be a preferential pathway for water and gas flow. Consequently, the EDZ could be a potential exit pathway for the radioactive waste to biosphere. An investigation of the Hydraulic-Mechanical (HM) and Thermal-Hydraulic-Mechanical-Chemical (THMC) behaviour of sedimentary rock formations is essential for the development of DGRs within such formations. This research work consists of (1) an experimental investigation of the mechanical behaviour of the anisotropic Tournemire argillite, (2) modeling of the mechanical behaviour of the Tournemire argillite, and (3) numerical simulations of the mechanical and hydromechanical behavior of two host sedimentary rocks, the Tournemire argillite and Cobourg limestone, for deep geological repository for nuclear wastes. The experimental program includes the measurements of the physical properties of the Tournemire argillite and its mechanical response to loading during uniaxial compression tests, triaxial compression tests with different confining pressures, unconfined and confined cyclic compression tests, Brazilian tests, and creep tests. Also, acoustic emission events are recorded to detect the initiation and propagation of microcracks within the rock during the uniaxial testing. The approach for modeling the mechanical behaviour of the Tournemire argillite consists of four components: elastic properties of the argillite, a damage model, the proposed concept of mobilized strength parameters, and the classical theory of elastoplasticity. The combination of the four components results in an elastoplastic-damage model for describing the mechanical behaviour of the Tournemire argillite. The capabilities of the model are evaluated by simulating laboratory experiments. Numerical simulations consist of: (1) a numerical simulation of a mine-by-test experiment at the Tournemire site (France), and (2) numerical simulations of the mechanical and hydromechanical behaviour of the Cobourg limestone within the EDZ (Canada). The parameters influencing the initiation and evolution of EDZ over time in sedimentary rocks are discussed.

Receptores nucleares formam uma superfamília de proteínas responsáveis pela regulação da expressão de genes. Estruturalmente, são formados por três domínios: um domínio N-terminal bastante variável, um domínio altamente conservado de ligação com o DNA e um domínio C-terminal, menos conservado, denominado domínio de ligação com o ligante (LDB). Diversos experimentos mostram que a interação com o ligante afeta a estrutura e a mobilidade da hélice C-terminal dos receptores nucleares (hélice 12 do domínio de ligação com o ligante), sendo o principal mecanismo de ativação e repressão da transcrição. As primeiras estruturas de LBDs de receptores nucleares revelaram importantes diferenças entre estruturas contendo ligantes (holo) e estruturas apo, principalmente no que diz respeito a posição da hélice 12: em estruturas apo, foi observada a H12 em uma conformação aberta, expondo o sítio de ligação com o ligante, enquanto que em estruturas holo, foi observada a H12 em uma conformação fechada, dobrada sobre o corpo do LBD e envolvendo completamente o ligante. Essa diferença sugeriu um mecanismo para a entrada e saída de ligantes do sítio de ligação denominado modelo da ratoeira, entretanto, esse modelo apresenta diversas inconsistências e tem sido desacreditado. Estudos experimentais e teóricos recentes mostram que a hélice 12 é mais móvel na ausência de ligantes, entretanto, esses estudos não fornecem evidencias de que o aumento da mobilidade da está associado com o deslocamento da H12 em relação ao corpo do LBD, como sugerido pelo modelo da ratoeira. Embora esteja claro que a hélice 12 é mais móvel na ausência de ligantes, a dimensão da variação conformacional sofrida pela hélice 12 ainda não está clara. Nesse trabalho buscamos a construção de um modelo capaz de dimensionar a mobilidade da hélice 12 através da comparação direta entre simulações de dinâmica molecular e experimentos de anisotropia de fluorescência resolvida no tempo. Utilizando simulações de dinâmica molecular reproduzimos experimentos de anisotropia de fluorescência acoplando a sonda cys-flúor a hélice 12 do PPARγ para estudar sua mobilidade. Mostramos que as observações experimentais só podem ser explicadas por conformações onde a sonda fluorescente permanece presa a superfície do LBD. Foi mostrado também que curvas de anisotropia com decaimentos comparáveis com os decaimentos experimentais estão associados a pequenas variações conformacionais de hélice 12. Simulações para dois modelos de apo-PPARγ com a H12 aberta em relação ao corpo do LBD e para as estruturas cristalográficas de apo-RXR e apo-ER, onde a H12 também adota uma conformação aberta, revelaram curvas de anisotropia com decaimentos mais rápidos que os experimentais. Esses resultados implicam em um modelo onde a H12 sofre alterações conformacionais locais, não apresentando variações tão dramáticas como o proposto pelo modelo da ratoeira.
Nuclear Hormone Receptors comprise a protein superfamily responsible for regulation of gene expression. Structurally, they are composed by three domains: a variable N-terminal domain, a highly conserved DNA-binding domain (DBD), and a less conserved C-terminal domain, known as ligand binding domain (LBD). Many experiments have shown that the interaction with ligands affects the structure and the mobility of nuclear receptors C-terminal helix (LBDs Helix 12), being the main mechanism of transcription activation and repression. The first nuclear receptor LBDs structures revealed important differences between ligand bound (holo) and apo-structures concerning the position of the H12: in apo structures, H12 adopted an open conformation, exposing the ligand binding pocket, whereas in holo structures, the H12 was closed, packed over the body of the LBD, burying completely the ligand. This difference suggested a mechanism for ligand entry and exit from the binding pocket called mouse-trap model, however this model has several inconsistencies and has been discredited. Recent experimental and theoretical studies have shown that H12 is more labile in the absence of ligand, but these studies dont provide evidences that the increase in the mobility is associated with the detachment of H12 from the body of the LBD as suggested by the mouse-trap model. Although its clear that H12 is more flexible in the absence of ligands, the size of the conformational changes undergone by H12 is not yet clear. In this work we seek to construct a definitive model for the range of motions that H12 may undergo in the presence or absence of ligand using molecular dynamics simulations. Through direct comparison between molecular dynamics simulations and time-resolved fluorescence anisotropy experiments, we show that experimental observation can only be explained by conformations where the fluorescent probe is interacting with the surface of the PPARγ surface. We also show that simulations with anisotropy decay rates comparable to the experimental decay are associated with small helix 12 conformational changes. Simulations with two models of apo-PPARγ with H12 detached from the body of the LBD and with crystallographic structures of apo-RXR and apo-ER, where the H12 also is in an open conformation, display anisotropy decay rates significantly faster than the experimental ones. These results imply a model for the molecular mobility of the LBD where H12 undergoes local conformational changes and should exhibit dynamic properties less dramatic than proposed by the mouse trap model.

La presente tesis doctoral se centra en el estudio de técnicas de mejora de resolución de la espectroscopía por Resonancia Magnética Nuclear (RMN) para una más simple y precisa elucidación estructural de moléculas pequeñas. El trabajo se ha presentado como un compendio de siete publicaciones escritas para diversas prestigiosas revistas científicas. Las publicaciones desarrollan en profundidad la aplicación de las mejoras de resolución para i) una medida precisa y eficiente de las constantes de acoplamiento tanto homo- como heteronucleares e ii) la optimización de las medidas de parámetros anisotrópicos a través de medios débilmente alineados. Estos dos tópicos se desarrollan mediante: 1. La aplicación de modernas técnicas de RMN para la mejora de laresolución, tanto digital como de señal, en experimentos 2D sin comprometer el tiempo experimental. 2. El diseño de nuevas secuencias de pulsos para la medida de conectividades de largo alcance heteronuclear. 3. La implementación de secuencias de pulsos ya existentes y el diseño de nuevas para el estudio de muestra en medio aniostrópicos. 4. El estudio de nuevos métodos en RMN para la discriminación mediante parámetros anisotrópicos. 5. La aplicación de protocolos para la automatización y simplificación de las medidas de contantes de acomplamientos en medio isotrópicos y anisotrópicos.
The present doctoral thesis is focused on the study of resolution-enhanced techniques for Nuclear Magnetic Resonance (NMR) spectroscopy in order to achieve a simpler and more precise structural elucidation of small molecules. The work has been presented as a compendium of seven publications written in several prestigious scientific journals. The publications develop in depth the application of resolution improvements for i) a precise and efficient measurement of homo- and heteronuclear coupling constants and ii) an optimization of anisotropic parameter measurements through weakly aligned means. These two topics are developed by: 1. The practical implementation of modern NMR techniques to improve the digital and signal resolution of 2D experiments without compromising the experimental time. 2. The design of improved pulse sequences to achieve the measurement of longer- range heteronuclear connectivities. 3. Implementation of novel NMR approaches to study samples in anisotropic environments, as well as the design of new pulse sequences adapted to the experimental measurement of NMR parameters in these media. 4. Evaluation of new NMR strategies for efficient structure discrimination using anisotropic NMR parameters. 5. Application of protocols for the easy automatization and measurement of coupling constants in isotropic and anisotropic media.

Les récepteurs nucléaires sont membres d'une famille de protéines activées par des ligands et qui régulent la transcription de nombreux gènes. Le récepteur nucléaire RevErbα est constitutivement inhibiteur de la transcription de gènes cibles via le recrutement du complexe corépresseur NCor-HDAC3 (Nuclear CoRepressor et Histone DeAcetylase 3). Ce complexe joue un rôle important dans le contrôle de l'horloge circadienne et de la glucogenèse via la régulation de la transcription des gènes codant pour les enzymes G6Pase (Glucose-6-Phosphatase) et PEPCK (PhosphoEnol Pyruvate Carboxy Kinase). Ces deux enzymes sont impliquées dans la glucogénèse qui est dérégulée en cas de diabète de type 2. Ce travail est basé sur l'investigation de l'interaction du récepteur nucléaire RevErbα avec deux corépresseurs: son partenaire établit NCor et SMRT (Silencing Mediator for Retinoid and Thyroid Receptors). Malgré ce qui est rapporté dans la littérature, c'est à dire que SMRT et RevErbα n'interagissent pas fonctionnellement in vivo, nous avons choisis d'étudier cette interaction à cause de la similarité de séquence entre les deux corépresseurs, mais également parce que les peptides des deux corépresseurs ont été rapportés comme interagissant avec d'autre récepteurs nucléaire. Afin d'étudier ces interactions, nous avons utilisé deux techniques complémentaires basées sur l'émission de fluorescence: Une technique in vitro qui est l'anisotropie de fluorescence et une technique de microscopie de fluorescence in cellulo appelée Number & Brightness. En plus de cette étude de l'interaction entre le récepteur nucléaire et les corépresseurs, nous nous sommes intéressé à déterminer l'effet de plusieurs ligands sur cette interaction. Trois ligands ont été testés: l'hème qui est rapporté comme étant le ligand naturel de RevErbα et deux ligands synthétiques et non naturels de RevErbα (SGN et SD7). Grâce à l'anisotropie de fluorescence (in vitro), nous avons confirmé et quantifié l'interaction entre le domaine de liaison au ligand (LBD) de RevErbα et un peptide NCor contenant le domaine d'interaction majeur (ID1 pour RevErbα et nous avons déterminé l'effet des trois ligands sur cette interaction. Nous avons également quantifié l'interaction entre RevErbα et d'autres peptides provenant de NCor et correspondant aux autres domaines d'interaction (ID2 et ID3) pour sa liaison à RevErbα. Nous avons déterminé que l'hème et le SD7 ont un effet déstabilisateur de la liaison de RevErbα à NCor in vitro, alors que le ligand SGN améliore la stabilité de complexe. Nous avons également confirmé une interaction entre RevErbα et un peptide corépresseur issu de SMRT. Afin d'étudier l'interactions des protéines pleine taille dans un contexte plus fonctionnel, nous avons utilisé le 2 photons-2 couleurs Number & Brightness. C'est une technique de microscopie à fluorescence basée sur la fluctuation de l'intensité de fluorescence pour étudier les interactions spécifiques de RevErbα avec NCor et SMRT pleine taille in cellulo ainsi que l'effet des ligands, précédemment mentionné, sur ces interactions. Dans les conditions choisies pour notre étude, nous avons déterminé que RevErbα interagit fortement avec NCor in cellulo et que cette interaction est améliorée par le ligand SGN. En revanche, l'hème et le SD7 n'ont pas d'effet observable sur ce complexe. Nous avons également montré pour la première fois que RevErbα forme des complexes avec le corépresseur SMRT pleine taille in cellulo. La continuité de ce travail pourrait être ciblée sur l'identification de ligands qui augmenterait le recrutement du complexe corépresseur NCor-HDAC3 sur RevErbα, menant ainsi à la diminution de l'expression des gènes cibles. En définitive, un ligand tel que celui-ci pourrait être d'un grand intérêt dans la recherche de la diminution de glucose dans le sang dans les cas de diabètes de type 2
Nuclear receptors are members of ligand-inducible factors that regulate the transcription of many genes. Nuclear receptor RevErbα constitutively inhibits the transcription of target genes via the recruitment of the corepressor complex NCor-HDAC3 (Nuclear CoRepressor and Histone DeAcetylase 3). This complex plays an important role in controlling the circadian clock and glucogenesis via regulation of the transcription of the G6Pase (Glucose-6-Phosphatase) and PEPCK (PhosphoEnol Pyruvate Carboxy Kinase) genes, both coding for proteins involved in glucogenesis, which is central to type 2 diabetes. Here we have investigated the interaction of the nuclear receptor RevErbα with two corepressors: its establish partner, NCor and SMRT (Silencing Mediator for Retinoid and Thyroid Receptors). Despite literature reports that SMRT and RevErbα do not interact functionally in vivo, we choose to study this interaction because of sequence similarity between the two corepressors, because peptides of both corepressors were reported to interact with other nuclear receptors. To investigate these interactions, we used two complementary fluorescence techniques: In vitro assays based on fluorescence anisotropy and an in cellulo fluorescence microscopy technique called Number & Brightness. In addition to the interactions between the CoRs and the RN, we were interested in determining the effects of several ligands on these interaction. Three ligands were tested: heme, which is reported to be the natural ligand of RevErbα and two synthetic and non-naturals ligands of RevErbα (SGN and SD7). By fluorescence anisotropy (in vitro) we confirmed and quantitated the interaction between purified RevErbα Ligand Binding Domain (LBD) and an NCoR peptide containing the major interaction domains (ID1) for RevErbα and revealed the effect of the three ligands on this interaction. We quantitated as well, the interaction between RevErbα and other peptides from NCor corresponding to the other interaction domains (ID2 and ID3) for it binding to RevErbα. We found a destabilizing effect of heme and SD7 binding to RevErbα on it interaction with NCor in vitro, whereas the ligand SGN enhanced the complex stability. We also confirmed an interaction between RevErbα and a SMRT peptide corepressor in vitro. In order to examine these interactions in a more functionally relevant context using full length proteins, we used 2 photon 2 colors Cross Number and Brightness (N&B), an fluorescence microscopy technique based on fluorescence intensity fluctuations to study specific interactions of full length RevErbα with NCor and SMRT in cellulo as well as the effect of several ligands above mentioned. Under the conditions of our studies, we find that RevErbα and NCor interact strongly in cellulo, and we observed a slight enhancement of this interaction by the SGN ligand. No effect of heme or SD7 was observed on the complex. We show as well for the first time that RevErbα forms complexes with the full length SMRT corepressor in cellulo. Future extensions of these studies could be aimed at identifying ligands that enhance the recruitment of the corepressor complex NCor/HDAC3 by RevErbα, thus leading to a decrease expression of the target genes. Ultimately such a ligand could be of interest in the quest to decrease blood glucose levels in type 2 diabetes

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Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico
The effect of confinement on the magnetic structure of vortices of dipolar coupled ferromagnetic nanoelements is an issue of current interest, not only for academic reasons, but also for the potential impact in a number of promising applications. Most applications, such as nano-oscillators for wireless data transmission, benefit from the possibility of tailoring the vortex core magnetic pattern. We report a theoretical study of vortex nucleation in pairs of coaxial iron and Permalloy cylinders, with diameters ranging from 21nm to 150nm, and 12nm and 21nm thicknesses, separated by a non-magnetic layer. 12nm thick iron and Permalloy isolated (single) cylinders do not hold a vortex, and 21nm isolated cylinders hold a vortex. Our results indicate that one may tailor the magnetic structure of the vortices, and the relative chirality, by selecting the thickness of the non-magnetic spacer and the values of the cylinders diameters and thicknesses. Also, the dipolar interaction may induce vortex formation in pairs of 12nm thick nanocylinders and inhibit the formation of vortices in pairs of 21nm thick nanocylinders. These new phases are formed according to the value of the distance between the cylinderes. Furthermore, we show that the preparation route may control relative chirality and polarity of the vortex pair. For instance: by saturating a pair of Fe 81nm diameter, 21nm thickness cylinders, along the crystalline anisotropy direction, a pair of 36nm core diameter vortices, with same chirality and polarity is prepared. By saturating along the perpendicular direction, one prepares a 30nm diameter core vortex pair, with opposite chirality and opposite polarity. We also present a theoretical discussion of the impact of vortices on the thermal hysteresis of a pair of interface biased elliptical iron nanoelements, separated by an ultrathin nonmagnetic insulating layer. We have found that iron nanoelements exchange coupled to a noncompensated NiO substrate, display thermal hysteresis at room temperature, well below the iron Curie temperature. The thermal hysteresis consists in different sequences of magnetic states in the heating and cooling branches of a thermal loop, and originates in the thermal reduction of the interface field, and on the rearrangements of the magnetic structure at high temperatures, 5 produce by the strong dipolar coupling. The width of the thermal hysteresis varies from 500 K to 100 K for lateral dimensions of 125 nm x 65 nm and 145 nm x 65 nm. We focus on the thermal effects on two particular states: the antiparallel state, which has, at low temperatures, the interface biased nanoelement with the magnetization aligned with the interface field and the second nanoelement aligned opposite to the interface field; and in the parallel state, which has both nanoelements with the magnetization aligned with the interface field at low temperatures. We show that the dipolar interaction leads to enhanced thermal stability of the antiparallel state, and reduces the thermal stability of the parallel state. These states are the key phases in the application of pairs of ferromagnetic nanoelements, separated by a thin insulating layer, for tunneling magnetic memory cells. We have found that for a pair of 125nm x 65nm nanoelements, separated by 1.1nm, and low temperature interface field strength of 5.88kOe, the low temperature state (T = 100K) consists of a pair of nearly parallel buckle-states. This low temperature phase is kept with minor changes up to T= 249 K when the magnetization is reduced to 50% of the low temperature value due to nucleation of a vortex centered around the middle of the free surface nanoelement. By further increasing the temperature, there is another small change in the magnetization due to vortex motion. Apart from minor changes in the vortex position, the high temperature vortex state remains stable, in the cooling branch, down to low temperatures. We note that wide loop thermal hysteresis may pose limits on the design of tunneling magnetic memory cells
Os efeitos de confinamento e o forte acoplamento dipolar na estrutura de v?rtices de nano-elementos ferromagn?ticos ? um tema de interesse atual, n?o apenas pelo valor puramente acad?mico, mas tamb?m pelo impacto em grande n?mero de dispositivos da ?rea de spintr?nica. Muitos dispositivos, como nano-osciladores para transmiss?o de dados sem fio, podem tirar grande proveito da possibilidade de controlar o padr?o magn?tico do n?cleo do v?rtice magn?tico. Relatamos um estudo te?rico da nuclea??o de v?rtices em um par de cilindros coaxiais de ferro e de Permalloy, com di?metros desde 21nm at? 150nm e espessuras de 12nm e de 21nm, separados por uma fina camada n?o-magn?tica. Cilindros isolados de ferro e Permalloy com espessura de 12nm n?o permitem a forma??o de v?rtices, enquanto que cilindros de espessura de 21nm possuem v?rtices quando isolados em reman?ncia. Nossos resultados indicam que ? poss?vel controlar a estrutura magn?tica dos v?rtices, bem como a chiralidade e polaridade relativa dos dois v?rtices, pela escolha apropriada dos valores dos di?metros e da separa??o dos dois cilindros ferromagn?ticos. Dependendo do valor da separa??o entre os cilindros, a intera??o dipolar pode induzir a forma??o de v?rtices em pares de cilindros de espessura de 12nm e inibir a forma??o de v?rtices em pares de cilindros de 21nm de espessura. Al?m disso, mostramos que a rota de prepara??o do estado magn?tico em campo nulo, pode ser usada para determinar a chiralidade e polaridade relativa dos dois v?rtices. Por exemplo: partindo da satura??o da magnetiza??o de um par de cilindros de ferro com di?metro de 81nm e espessura de 21nm, na dire??o do eixo f?cil da anisotropia uniaxial do ferro, resulta um par de v?rtices com n?cleo de 36nm, mesma chiralidade e mesma polaridade. Partindo do estado saturado em uma dire??o no plano e perpendicular ao eixo de anisotropia uniaxial, resulta um par de v?rtices com n?cleo de 30nm de di?metro, com chiralidade e polaridade opostas. Relatamos tamb?m um estudo te?rico do impacto de v?rtices magn?ticos na histerese t?rmica de um par de nanoelementos el?pticos de ferro, de 10nm de espessura, separados por um espa?ador n?o-magn?tico e acoplados com um substrato antiferromagn?tico por energia de 3 troca. Nossos resultados indicam que h? histerese t?rmica em temperatura ambiente (muito menor do que a temperatura de Curie do ferro), se o substrato for uma superf?cie n?o compensada de NiO. A histerese t?rmica consiste na diferen?a da sequ?ncia de estados magn?ticos nos ramos de aquecimento e resfriamento de um ciclo t?rmico, e se origina na redu??o do valor do campo de interface em altas temperaturas, e na reestrutura??o das fases magn?ticas impostas pela intera??o dipolar forte entre os dois nanoelementos de ferro. A largura da histerese t?rmica varia entre 500K ? 100K para dimens?es laterais de 125nm x 65nm e 145nm x 65nm. Focamos nos ciclos t?rmicos de dois estados especiais: o estado antiparalelo, com o nanoelmento em contato com o substrato alinhado na dire??o do campo de interface e o outro nanoelemento alinhado em dire??o oposta; e o estado paralelo em que os dois nanoelementos est?o alinhados com o campo de interface em temperaturas baixas. Esses s?o os dois estados magn?ticos b?sicos de c?lulas de mem?rias magn?ticas de tunelamento. Mostramos que a intera??o dipolar confere estabilidade t?rmica ao estado antiparalelo e reduz a estabilidade t?rmica do estado paralelo. Al?m disso, nossos resultados indicam que um par de cilindros com dimens?es de 125nm x 65nm, separados por 1.1nm, com campo de interface de 5.88kOe em temperatura de 100K, est? no estado paralelo. Essa fase se mant?m at? 249K, quando h? uma redu??o de 50% da magnetiza??o devido ? nuclea??o de um v?rtice no nanoelemento com superf?cie livre. Pequenas varia??es da magnetiza??o, devidas ao movimento do v?rtice, s?o encontradas no ramo de aquecimento, at? 600K. O estado encontrado em 600K se mant?m ao longo do ramo de resfriamento, com pequenas mudan?as na posi??o do v?rtice. A exist?ncia de histerese t?rmica pode ser um s?rio limite de viabilidade de mem?rias magn?ticas de tunelamento

Abstract The subjects of this thesis are the dynamics of liquid crystals in external electric and magnetic fields as well as the magnetic properties of small molecules, both studied by liquid crystal nuclear magnetic resonance (LC NMR) spectroscopy. Director dynamics of a liquid crystal 5CB in external magnetic and electric fields was studied by deuterium NMR and spectral simulations. A new theory was developed to explain the peculiar oscillations observed in the experimental spectra collected during fast director rotation. A spectral simulation program based on this new theory was developed and the outcome of the simulations was compared with the experimental results to verify the tenability of the theory. In the studies on the properties of small solute molecules, LC NMR was utilised to obtain information about anisotropic nuclear magnetic interaction tensors. The nuclear magnetic shielding tensor was studied in methyl halides, the spin-spin coupling tensor in methyl mercury halides and the quadrupolar coupling tensor in deuterated benzenes. The effects of small-amplitude molecular motions and solvent interactions on the obtained parameters were considered in each case. Finally, the experimental results were compared to the corresponding computational NMR parameters calculated in parallel with the experimental work.

Les réacteurs nucléaires refroidis au sodium offrent des perspectives intéressantes pour la filière nucléaire (utilisation optimale de l'uranium naturel, réduction de la radiotoxicité des déchets nucléaires). Cependant, la nécessité d’élever le niveau de sûreté de ces réacteurs aux standards du XXIe siècle a conduit à des designs de cœurs très hétérogènes.Ainsi, les objectifs de la thèse sont l’identification des principaux phénomènes physiques devant être pris en compte lors du calcul neutronique de cœurs hétérogènes en spectre rapide, ainsi que le développement de schémas de calcul adaptés dans le code APOLLO3 du CEA. Après quelques rappels théoriques et méthodologiques, ce document présente une analyse critique des schémas de calcul disponibles dans APOLLO3 pour les réacteurs refroidis au sodium. Cette analyse permet de mettre en évidence la nécessité de simuler, dès l’étape de préparation des sections efficaces, des modes angulaires du flux qui soient représentatifs de la configuration géométrique du cœur. Pour répondre à ce besoin dans le cadre de géométries présentant une forte hétérogénéité axiale, une approximation 2D/1D à l'équation du transport des neutrons 3D est développée. Cette dernière permet de représenter de manière cohérente, et à moindre coût, des effets d’anisotropie axiale dans des calculs 2D. Une nouvelle modélisation de type traverse de l’interface cœur / réflecteur est également proposée, ainsi qu’une méthode de calcul innovante des barres de contrôle. Ces méthodes permettent, in fine, de définir un schéma de calcul de référence unique et validé numériquement, adapté à la modélisation des cœurs de réacteurs refroidis au sodium
Sodium-cooled nuclear reactors offer interesting perspectives in terms of uranium resources economy and radioactive waste management. In order to meet modern safety standards, though, increasingly complex core concepts have been proposed for this technology.Hence, the first objective of this thesis is the identification of the main physical phenomena that need to be taken into account when modeling the neutronic behavior of a heterogeneous nuclear core in a fast neutron spectrum. The second objective is the development of appropriate calculation schemes in the APOLLO3 code, developed at CEA.After a brief reminder of neutronic calculation theory and methods, this document presents a critical analysis of the neutronic calculation schemes available in APOLLO3 for sodium-cooled applications. This analysis highlights the necessity to model, during the cross section preparation phase, angular modes of the neutron flux that are representative of the core geometrical configuration. To meet this need in axially heterogeneous geometries, a 2D/1D approximation to the 3D neutron transport equation is derived and implemented in APOLLO3. In particular, it is shown that this approximation allows to consistently represent axial angular modes of the flux in 2D calculation domains. Besides, a new traverse model is proposed for the core/reflector radial interface, as well as an innovative control rod calculation method. The combination of these methods allows to define a unique, and numerically validated, reference calculation scheme in APOLLO3, suitable for the calculation of a wide range of complex sodium-cooled nuclear cores

Le contrôle spatial et temporel de l'auto-assemblage de molécules fluorescentes en nano-objets organisés et en matériaux mous a été réalisé par photochimie.La photodécarbonylation quantitative du progélifiant dkDDOA sous irradiation génère le super gélifiant 2,3-didécyloxyanthracène (DDOA) à température ambiante et simultanément gélifie le DMSO. DkDDOA est réactif sous excitation avec de la lumière bleue en raison de la fonction alpha-dicétone sensible à la lumière qui est ajoutée au noyau aromatique. De plus,l’ajustement de la couleur de l'émission du gel du bleu au vert a été obtenu en ajoutant un dérivé 1,2-dicétone-5,12-diphényltétracène photo réactif qui donne un 5,12-diphényltétracène émissif vert sensibilisé par un transfert d'énergie efficace.Sous un microscope, l'irradiation laser focalisée permet la structuration de nanofibres émissives sur une surface de verre. Bien que la surface de verre soit non traitée, on peut obtenir des micropattern de nanofibres de DDOA hautement alignées. Ces surfaces émettent une lumière bleue polarisée linéairement, comme le prouve la microscopie de polarisation. L'anisotropie élevée et l'orientation des fibres ont été obtenues en contrôlant la densité de nucléation et la direction de balayage du laser focalisé. Des micropattern orientés perpendiculairement peuvent ainsi être juxtaposés sur la même surface
The spatial and temporal control of the self-assembly of fluorescent molecules into organized nano-objects and into soft materials was achieved by photochemistry. The quantitative photodecarbonylation of the progelator dkDDOA under irradiation generates the supergelator 2,3-didecyloxyanthracene (DDOA) at room temperature and simultaneously gelates DMSO. dkDDOA is reactive under excitation withblue light due to the light sensitive alpha-diketone moiety that is added to the aromatic core.Additional colour-tuning from blue to green emission from the gel was achieved by adding a similar photoreactive 1,2-diketone-5,12-diphenyltetracene that yields a green emissive 5,12-diphenyltetracene sensitized through an efficient energy transfer. Under a microscope, focused laser irradiation enables the patterning of blue-emissive nanofibers on to a glass surface. Although the surface is non-treated, micropatterns of highly aligned DDOA nanofibers can be obtained. These surfaces emit linearly polarized blue light,as proven with polarization microscopy. The high anisotropy and the orientation of the fibers was achieved by controlling the nucleation density and the direction of scanning of the focused laser. Perpendicularly oriented micropatterns can thereby be juxtaposed on the same surface

La thèse porte sur la synthèse et l'étude des propriétés magnétiques de borates de fer-gallium,FexGa1-xBO3 avec 0 supérieur ou égal à x supérieur ou égal à 1. Ces matériaux sont prometteurs pour les applications; en plus, grâce à la présence, en fonction de x, de différents types d’ordre magnétique, ils sont bien adaptés au traitement de nombreux problèmes du magnétisme des solides.Le borate de fer, FeBO3 est un antiferromagnétique possédant un plan de facile aimantation et un faible ferromagnétisme. Les caractéristiques du borate de fer sont radicalement modifiées par substitution isomorphe fer – gallium diamagnétique.Nous avons mis au point une route de synthèse de monocristaux FexGa1-xBO3 de haute qualité. Comme principales techniques expérimentales, nous avons choisi les résonances magnétiques électronique (RME) et nucléaire (RMN). Selon le contenu du fer, nous avons observé:(i) la résonance antiferromagnétique, (ii) la résonance de clusters magnétiques et (iii) la résonance paramagnétique électronique (RPE). Les différents états magnétiques ont été identifiés et leurs caractéristiques – la température de Néel, le champ de Dzyaloshinskii-Moriya; les paramètres de l’hamiltonien de spin de Fe3+, etc.– ont été déterminées. La coordinence et la symétrie de sites de 11B et 71Ga ont été précisées par RMN à rotation sous l’angle « magique » (MAS). Moyennant la simulation des spectres de RPE et de MAS RMN, à l’aide de codes mis au point ad hoc, les distributions de paramètres dues au désordre local ont été déterminées. L’analyse théorique, tenant compte de contributions du champ cristallin et de l’interaction dipôle-dipôle, permet d’expliquer l’anisotropie magnétocristalline de volume et de surface
The thesis is concerned with synthesis and studying magnetic properties of iron-galliumborates, FexGa1-xBO3 with [0 supérieur ou égal à x supérieur ou égal à 1]. These materials are promising candidates for applications;besides, occurrence of different types of magnetic ordering, depending on x, makes them suitablefor treating a number of fundamental problems in solid state magnetism.Iron borate, FeBO3 is a two-sublattice easy-plane antiferromagnet with weakferromagnetism. Physical characteristics of iron borate are radically modified by isomorphoussubstitution of a part of iron by diamagnetic gallium.We have started with developing a synthesis route for growing high-quality FexGa1-xBO3single crystals. As main experimental techniques, we have chosen Electron and Nuclear MagneticResonances (EMR, NMR). Depending on iron contents and temperature, we have observed:(i) Antiferromagnetic, (ii) Cluster Magnetic and (iii) Electron Paramagnetic Resonance (EPR).Different magnetic states have been identified and their characteristics: Néel temperature,Dzyaloshinskii-Moriya field; spin Hamiltonian parameters of isolated Fe3+ ion, etc., have beendetermined. Coordination and site symmetry of 11B and 71Ga nuclei have been specified by meansof Magic Angle Spininng (MAS) NMR. Carrying out computer simulations of EPR and MASNMR spectra with laboratory-developed codes, the parameter distributions caused by localdisorder have been determined. Theoretical analysis taking into account crystal field and dipoledipolecontributions allow interpreting volume and surface magnetocrystalline anisotropy of thecrystals

Dans cette étude, nous analysons les conséquences mécaniques des transformations de phase diffusives, particulièrement la plasticité de transformation ou TRIP (TRansformation Induced Plasticity) ainsi que le comportement élasto-viscoplastique. Cette plasticité de transformation, explicable par le mécanisme de Greenwood-Johnson, est souvent décrite avec le modèle de Leblond qui fait l'hypothèse d'un comportement élastoplastique. Dans ce modèle comme dans la majorité des analyses expérimentales et des modélisations (analytiques, par éléments finis, FFT ou encore champ de phase), une des hypothèses principales est de ne pas prendre en compte le caractère visqueux du comportement. Or plusieurs études récentes montrent que le comportement des deux phases (parente et produite) peut être très sensible au taux de déformation imposé, particulièrement à haute température. D'où l'intérêt de développer une modélisation rendant compte des effets visqueux présents lors de certaines transformations. Pour ce faire, nous adoptons une modélisation numérique où le comportement de chaque phase est décrit par une loi élasto-viscoplastique à écrouissage mixte associée à la loi de Norton ; la cinétique de transformation est imposée et le problème d'interactions mécaniques entre phases est traité par la méthode des éléments finis. D'une part, la contribution de la viscosité au TRIP est quantifiée pour différents taux de déformation imposés durant la transformation de phase. D'autre part, l'effet du taux de transformation (configuration arbitraire) sur la prédiction du TRIP est évalué et caractérisé. Une extension des modèles existants (à cinétique périodique et aléatoire) est proposée. Elle consiste d'abord à étudier et évaluer l'effet de la morphologie de germe ainsi que l'anisotropie de croissance sur la prédiction du TRIP. Ensuite, une amélioration avec un modèle anisotherme, basé sur des mesures expérimentales existantes, a été introduite. Elle consiste principalement à tenir compte de la variation des propriétés mécaniques en fonction de la température. Les analyses montrent que la prise en compte de la viscosité peut conduire à des effets importants sur la prédiction du TRIP par rapport aux résultats obtenus avec un modèle élastoplastique classique. Elles montrent en particulier, en configuration anisotherme, une amélioration de la prédiction du TRIP mesuré expérimentalement lors de la transformation perlitique d'un acier 100Cr6 [Tahimi, 2012]. Cette étude permet par ailleurs de dégager des tendances évidentes dans les relations entre le TRIP et l'histoire de la transformation : chargement mécanique et cinétique de transformation, morphologie des germes et anisotropie de croissance. Ces résultats pourront contribuer à l'élaboration d'un modèle analytique simple prenant en compte la viscosité
In this study, the mechanical consequences of phase transformations in steel, particularly, the TRansformation Induced Plasticity TRIP as well as the elasto-viscoplastic behavior has been analyzed. This transformation plasticity, due to the Greenwood-Johnson mechanism, is often described with the model of Leblond with the assumption of an elastoplastic behavior. Moreover, in the majority of experimental analysis or numerical finite elements modeling FEM or phase field modeling PFM, the viscous criteria were not considered. However, several recent studies have demonstrated that both phases (parent and product) show high strain-rate sensitivity at elevated temperatures. Hence, the principal interests using the FEM modeling to extend these main reference models of [Leblond, 89] and [Taleb-Sidoroff, 2003], with taking into account the viscous effects, which are present during some phase transformations, especially at high temperatures. To do this, the behavior of each phase is described by an elasto-viscoplastic law with mixed hardening associated to the Norton law. The transformation kinetics is imposed and the problem of mechanical interactions between phases is processed by the finite element method. On the one hand, the contribution from viscosity to TRIP was quantified for different strain-rate during phase transformation. On the other hand, the effect of an arbitrarily-set of transformation-rate in the FEM simulations was evaluated and characterized. An extension of the existing models (for periodic and random kinetics) is proposed. It consists at first in studying and in evaluating the effect of both the morphology of nuclei and the growth anisotropy, on the prediction of TRIP. Then, an improvement with non-isothermal model, based on existing experimental measures, was introduced. It consists mainly in taking into account the variation of the mechanical properties of the mixture of both phases, according to the temperature. The predictions show that in such cases, the consideration of the viscosity can lead to major changes of the estimated TRIP compared with results obtained from a classic plastic model. Also, the prediction of TRIP can be significantly influenced by the choice of the morphology of germs and by the type of growth: isotropic or anisotropic. These improvements, particularly with the non-isothermal configuration, show a good agreement with experimental measures of TRIP on the 10006 steel during pearlite phase transformation [Tahimi, 2012]. This study allows besides, releasing obvious trends in the relations between the TRIP and the history of the phase transformation: mechanical loading and kinetics of transformation, morphology of nuclei and growth anisotropy. These results can contribute to the elaboration of a simple analytical model taking into account the viscous criteria

Nous avons réalisé des couches minces de Co sur un substrat semi-conducteur (Si(111)) par voix électrochimique, en mode potentiostatique et en mode galvanostatique, et étudié leurs propriétés topographiques (AFM, MEB) et magnétique (RMN, effet Kerr, SQUID), afin de relier ces propriétés aux modes de croissance et aux conditions de dépôt à priori identiques conduisent à des morphologies et donc des propriétés magnétiques très différentes. Nous avons développé une approche rigoureuse avec un contrôle systématique de la qualité du substrat de départ pour clarifier les modes de nucléation et de croissance en fonction du potentiel appliqué en chronoampérométrie. Une transition d’un mode de nucléation instantanée vers un mode de nucléation progressive en fonction du potentiel appliqué est mise en évidence. La modélisation à l’aide du modèle de Scharifker-Hills des modes de nucléation et de croissance est cohérente avec les images de topographie AFM. La croissance est tridimensionnelle du type Volmer-Weber et l’aimantation est orientée dans le plan. Par RMN et également X-Ray Photoemission Spectroscopy (XPS), nous montrons qu’une couche d’hydroxyde de cobalt magnétiquement morte se forme à l’interface avec le Si. En mode galvanostatique, des grains avec des facettes parfaitement cristallisés présentent des domaines magnétiques localisés dans la plupart des ilots. Nous avons également effectué une étude très critique des techniques de dépôt/arrachage employées dans la littérature montrant que celle-ci sont inadaptées aux substrats semi-conducteur, un dépôt subsistant sur la surface quel que soit la technique d’arrachage choisie
We have deposited thin layers of Co on a semiconductor substrate Si(111), by electrochemical method, in potentiostatic and galvanostatic mode, and we have studied their topographic properties (AFM, MEB) and magnetic (RMN, effet Kerr, SQUID). Thanks to these different techniques, we could relate these properties to the growth modes and to the a priori identical deposition conditions, which lead to different morphologies and therefore different magnetic properties. We have developed a rigorous approach with a systematic control of the quality of the substrate in order to clarify the nucleation and growth modes as a function of the potential applied in chronoamperometry. A transition from an instantaneous nucleation mode to a progressive nucleation mode as a function of the applied potential is highlighted. Modeling with Scharifker-Hills model of nucleation and growth modes is consistent with AFM topography images. The growth is three-dimensional of a Volmer-Weber type and the magnetization is oriented in the plane. By NMR and also X-Ray Photoemission Spectroscopy (XPS), we could show that a layer of magnetically dead cobalt hydroxide layer forms at the interface with Si. In galvanostatic mode, grains with perfectly crystallized facets have magnetic domains located in most of the islands. We have also carried out a very critical study of the deposition / tearing techniques used in the literature showing that they are unsuitable for semiconductor substrates, a deposit remaining on the surface whatever the tearing technique chosen

Movimentos coletivos prestam um papel fundamental na dinâmica e energética de biomoléculas em solução. Estes movimentos permitem o acoplamento de regiões significativamente distantes, apresentando considerável influência, por exemplo, no alosterismo para a formação de complexos macromoleculares e no funcionamento integrado de proteínas multidomínios como \"máquinas moleculares\". Neste trabalho de doutoramento, serão apresentados os resultados referentes à aplicação conjunta de técnicas experimentais biofísicas, de modelagem estrutural e de dinâmica molecular no estudo de dois sistemas para os quais estes movimentos coletivos demonstram considerável importância funcional. Para a interação do receptor nuclear do ácido 9-cis-retinóico com seu elemento responsivo específico no DNA (HRE), a comparação de estudos de dinâmica molecular com ensaios de afinidade por anisotropia de fluorescência sugere que a resistência inicial para a associação do monômero, seguida da acentuada colaboratividade na associação do dímero é regida por um impedimento da associação do domínio de ligação ao DNA (DBD) para o primeiro à sequência responsiva devido, em última análise, a uma não complementaridade dos modos coletivos mútuos. Este impedimento para a associação monomérica inicial é mais acentuado para o monômero 5\' (para o qual a menor especificidade de ligação à seqüência específica já é bem documentada), devido aos efeitos conjuntos de um \"defeito\" natural no empacotamento de bases da seqüência responsiva, que se manifesta mais significativamente na interface entre o meio-sítio 5\' e a seqüência espaçadora, e dos modos vibracionais entre os dois sítios decorrentes de seu faseamento relativo na topologia do DNA na seqüência responsiva, caracterizando um mecanismo \"chave e fechadura\" para a interação obrigatoriamente simultânea dos dois monômeros ao DNA. No segundo caso, um estudo integrado utilizando a técnica experimental de espalhamento de raios X a baixos ângulos e uma abordagem de modelagem estrutural baseada em dinâmica molecular foi realizado para a celobiohidrolase I de Trichoderma harziannum. Este estudo permitiu tanto a elaboração de um modelo estrutural de maior resolução para esta enzima de alto potencial biotecnológico como a constatação dos possíveis mecanismos moleculares a partir dos quais as glicosilações no peptídeo conector impõem restrições à orientação e modos vibracionais entre seus dois domínios de forma condizente com sua ação concertada na interação e no deslize da enzima sobre a superfície celulósica, ambos de fundamental importância para a processividade da enzima na hidrólise do substrato microcristalino.
Collective motions play a fundamental role in solution biomolecule dynamics and energetics. These movements can couple very distant regions in the protein structures affection, for instance, allosteric mechanisms, the establishment of macromolecular complexes, and on the integrated function of multidomain proteins as molecullar machines. In this thesis, we present results concerning to the joint use of experimental biophysical techniques, structural modeling and molecular dynamics simulations on the study of two systems for which these collective motions have substantial importance. First, we study the interaction of the nuclear retinoid X receptor with its specific DNA hormone response element (HRE) using a combination of molecular dynamics simulations and affinity assays performed by using fluorescence anisotropy. We find out that collective motions mediate the low binding affinity of monomers and the high cooperative binding of HRE dimers. The lower binding affinity of the monomer is more prominent for 5´ monomers. This occur due to an natural ineffective stacking of the last base pair step at the 5´-half-site and to the phasing of the two binding half-sites in the DNA topology, that impose a collective motions that tends to occlude the 5´ binding site. This behavior, in turn, is concurrent with the well known 3´ polarity and the decreased binding specificity to the 5´ half site for the hRXRα monomer. This same pattern impose a lock-and-key mechanisms dependent on the binding of the full dimer. Second, an integrated Small angle X ray scattering and molecular dynamics based structural modeling was used to comprehend the interdomain motions of cellobiohydrolase I of Trichoderma harziannum. We manage to build a refined model for this enzime, with important biotechnological potential. We also provide insights into molecular mechanisms of linker and glycosylation imposed restraints on the orientation and vibrational modes of the full-length enzyme, supporting a mechanism of sliding of on the cellulose surface. This mechanism is fundamental for the high processivity on the hydrolysis of microcrystalline cellulose.

碩士
國立成功大學
資源工程學系
104
After numerous years of international research and development, there is a broad technical consensus that deep geological disposal which offers relatively enough space to accommodate the large volume of HLW accumulated over the years will provide for the safety of humankind and the environment now and far into the future. In addition, there is not yet an operating geological repository for high-level radioactive waste, and there remains substantial public research about the underground rock mass of geological repository. However, most studies all consider the host rock as homogeneous and isotropic. While in real cases, underground host rock is inherently anisotropic and heterogeneous. Besides, many of them are thermally anisotropic, indicating that there is a preferred direction of thermal conductivity. Therefore, in this thesis, we extend the previous research (Salama A. et al., 2015) conducted to analyze thermal characteristics of HLW geological repositories by including the effect of anisotropy of thermal conductivity of host rock. We reveal that differences in anisotropy of thermal conductivity of host rock with direction could have clear effects on temperature fields. We also investigate the effect of dip angle on the temperature field. This includes 0⁰, 15⁰, 30⁰, 45⁰, 60⁰, 75⁰and 90⁰ in additions to the isotropic case as a reference. Furthermore, we also consider the effect of anisotropy ratio on the temperature fields. This includes ratios ranging from 1.1 to 1.5. The significant differences between this study with previous research are that we conducted the verification with analytical approach before the numerical simulation and also developed a chart for variation of peak rock wall temperature with the anisotropy ratio for different dip angles which can be used as an anisotropic case for HLW repositories reference. In order to ensure feasibility and accuracy of the numerical model, we conduct the numerical verification with analytical approach proposed by SKB (2009) before the thermal simulation for anisotropic cases. The results of both approaches show pretty much the same overall trends. As a result, after the verification, the same numerical model is feasibly used for the next anisotropic simulation. In this study, it is found that the temperature contours are shifted towards the direction of dip angle. The temperature of anisotropic cases are all high than isotropic one. Furthermore, the peak buffer temperature is found to be higher when the dip angle is larger and vice versa. Additionally, the peak buffer temperature is also found to be higher when anisotropic ratio is larger. Also we developed a chart of variation of peak buffer temperature with the anisotropy ratio for different dip angles and find that the peak buffer temperature meets the 100℃ design limit when anisotropy ratio is set to 1.3. The presented chart can be used as an anisotropic case for HLW repositories reference.

The thesis aims at methodological developments in Nuclear Magnetic Resonance (NMR) and study of oriented samples like liquid crystals and single crystals and powder samples. Though methodological development in solid state NMR (ss-NMR) has gone far ahead, this work attempts to contribute some novel methods in this direction. The work presented here falls into two categories (i) methodological developments for obtaining information on anisotropic interactions and (ii) experiments which utilize the existing methodologies to study systems of interest under static condition and also under sample spinning at the Magic Angle. In the solid state, dipolar couplings play a crucial role. On the one hand these couplings could be used to transfer polarization from an abundant nucleus to a rare nucleus and increase the sensitivity of the rare nucleus. On the other hand, the measurement of dipolar couplings itself is crucial for extracting structural and dynamic information. A third aspect is that dipolar couplings could be used to obtain correlation, say between two different nuclear species or between the same kind of nuclei as in an exchange experiment. A major part of this thesis deals with all three aspects mentioned above. The thesis presents a new heteronuclear polarization transfer scheme which is devoid of some of the short comings of the existing and well-known polarization transfer schemes. This pulse sequence has been found to be useful in different contexts involving both spin ½ and spin 1 nucleus. The use of dipolar couplings for obtaining correlation in both static oriented systems and in powder samples has been illustrated. In the case of the powder sample, the study has been useful in obtaining useful orientation information. Finally, chemical shifts are known to be indicators of finer structural features of molecules in solution and solid state. 13 C MAS NMR studies have been exploited in understanding these structural features of short peptides containing prolines in the solid state and for comparing with their structures in solution. Chapter 1 covers the theoretical aspects required for the experimental work described in the thesis. A brief description of NMR has been followed by the explicit description of various interaction Hamiltonian’s in ss-NMR. Subsequently the experimental and the theoretical tools needed for ss-NMR study like Magic Angle Spinning (MAS), Cross-Polarization, Homo/Heteronuclear decoupling schemes have also been discussed. Chapter 2, describes a new heteronuclear polarization transfer scheme for oriented samples – named DAPT (Dipolar Assisted Polarization Transfer) and its application to different systems. DAPT uses a homonuclear decoupling sequence such as BLEW-12 for effecting heteronuclear polarization transfer. The chapter has been divided into five related parts. Section 2(A) starts with an introduction to the existing heteronuclear polarization transfer schemes. Subsequently the theoretical background of the new sequence is presented. Experimental implementation of the sequence in an oriented system, liquid crystal is presented and is compared with the well-known polarization transfer scheme, Hartmann-Hahn Cross Polarization (HH-CP). In 2(B) the implementation of the sequence as a local field spectroscopy for measuring heteronuclear dipolar couplings is presented. After initial discussion about local field spectroscopy and its relevance in ss-NMR, the improvements made in the earlier mentioned sequence along with its 2D implementation in a liquid crystal sample are described. A comparative study is also presented using DAPT with various other homonuclear decoupling sequences. Chapter 2(C) deals with the extension of DAPT to spin-1 systems. The difficulties in setting up the HH-CP in spin-1 systems are highlighted. Experimental demonstrations on a test sample of oriented CD3 I and also on a deuterated liquid crystal is described. The sequence has been incorporated as part of a 2D correlation experiment, where the F1 dimension provides the quadrupolar couplings of deuterium and the F2 the chemical shifts of the attached carbons. The comparison of the sequence with HH-CP, its merits and demerits are discussed and the potential applications are highlighted. Chapter 2(D) deals with the relatively less studied transition in 14N nucleus, known as the Overtone-Transition (OT). An introduction to OT and its relevance is provided in the beginning followed by the extension of DAPT in exciting and detecting OT. The experiments have been done on a single crystal of a model peptide, N-Acetyl-DL-Valine and are compared with the conventional method. Amide proton chemical shifts are also measured using DAPT in an indirect way. The advantages and the future application in studying OT are also discussed. Chapter 2(E) discusses the extension of DAPT to the single crystal of NAV and in identifying the molecules in the unit cell. The SLF spectrum of NAV is complicated due to the presence of two magnetically in-equivalent molecules in the unit cell and with pairs of splitting for each C - 1H and C - 1H pairs. The dipolar couplings are extracted from the experiment and with the aid of a MATLAB program and by incorporating the crystal coordinates, identification of C-1H and C-1H pairs belonging to a particular molecule have been carried out. Chapter 3 describes a novel and useful modification of the well-known Separated Local Field (SLF) sequence in solid state known as PISEMA (Polarization Spin Exchange at the Magic Angle). PISEMA is a popular technique for measuring heteronuclear dipolar couplings in oriented in oriented biological membranes and in liquid crystals. While it has several advantages such as a large dipolar scaling factor, narrow line-widths in the dipolar dimension and ease of setting up etc it suffers from a major problem. The technique is highly sensitive to the proton off-sets which affect the measured dipolar couplings. In the present chapter the origin of this problem has been analyzed in detail and a solution has been proposed. The modification to the experiment has been implemented on a liquid crystal and the off-set independence of the new sequence has been demonstrated. Further studies on a more rigid system such as a solid single crystal has been used to verify the effect of the modification on homonuclear decoupling efficiency and the consequent effects on the line widths in addition to off-set independence. The advantages of the proposed method over the existing one in terms of line-width and robustness in measuring heteronuclear dipolar couplings are demonstrated. Chapter 4 presents a study of deuterium exchange on a di-peptide. Deuterium as well as carbon-13 NMR spectroscopy has been extensively used earlier on static powder samples for studying exchange phenomena. In the present study we have applied the methodology for obtaining relative N-D vector orientation in a di-peptide. The magnetization exchange between deuterium nuclei through the dipolar couplings between them has been monitored. The need to match the quadrupolar split energy levels of two different deuterium’s differently oriented in the magnetic field requires that the sample be spun slowly. Characteristic exchange powder patterns were obtained which were used to infer relative orientation information. Comparison with the crystal structure indicates that the magnetization is likely to be inter-molecular rather than intra-molecular. The chapter follows the following sequence. A brief description about the importance of exchange studies in ss-NMR is presented. A theoretical approach is followed by a discussion of the angular dependence of the frequencies and the visualization of the mutual re-orientation angles. The motivation of the project followed by the experimental techniques, especially the use of slow MAS ~ 100 Hz in exchange studies are also presented. Initial studies have been carried out on di-methyl sulphone to check the reproducibility of the earlier reported results and later the sequence is extended to amide proton deuterated di-glycine. The 2D exchange spectrum recorded under slow MAS is then discussed in the context of the crystal structure and possible amide deuteriums involved in the exchange process are inferred. Chapter 5 discusses the natural abundant 13C and 15N NMR spectroscopy in the solid state in designed tri-peptides containing prolines. Proline is a unique amino acid because of it torsion angle values and is responsible for the turns and the globularity of the proteins. The well studied SH3 domain protein often binds to short peptides containing prolines and hence these study gains importance. Three peptides containing prolines were taken up for study. For peptide (1), the conformation was observed as cis/trans in the solution state and for the other two peptides it was all trans. The X-ray studies showed that peptide (1) has two molecules in the unit cell with both cis conformation. This motivated us to look at the solid state spectra of the peptides. Chemical shifts are signatures of conformers and it was established from the chemical shift differences that there exist two molecules in the unit cell for peptide (1), both in cis conformation. The conformers for the other two peptides predicted by NMR chemical shifts also matched with those obtained from X-ray studies. This opens up the possibility of using simple NMR measurements in the solid state as tools for secondary structure determination in larger peptides and proteins.

This thesis investigates the differences in Bonner Sphere detector response for anisotropic neutron fields as a function of borehole orientation. Monte Carlo simulations using MCNPX were used to calculate the difference for a borehole oriented directly behind a unidirectional neutron field and one in which the borehole is normal to the neutron flux. The differences in detector response depend on the size of the Bonner Sphere and the energy of the incident flux, which could introduce significant error in the determination of the neutron field’s energy spectrum.