Neste trabalho foi desenvolvido um estudo sistemático dos mecanismos de difusão responsáveis pelo switching de resistência em memórias resistivas. Essas memórias possuem estrutura semelhante a de um capacitor, a qual sofre uma transição de resistência induzida pela aplicação de um campo elétrico. A transição é provocada pela formação de filamentos condutivos no interior da matriz semicondutora. Os filamentos podem ser constituídos por metal originado de um dos eletrodos (ECM) ou por regiões do óxido deficientes em oxigênio (VCM), geradas pela difusão de vacâncias de oxigênio. Dispositivos de TiO2 foram construídos e sua resposta elétrica foi adquirida através de medidas elétricas do tipo I-V para diferentes metais de eletrodo. Técnicas de análise por feixe de íons, como retroespalhamento Rutherford por micro-feixe e perfilometria com reação nuclear ressonante, foram usadas para detalhamento dos processos de difusão. Constatou-se uma dependência do comportamento elétrico em função do método de deposição da camada semicondutora, sua espessura e os parâmetros da medida de tensão. No caso do filamento ser composto por átomos de metal, espectros de micro-RBS foram adquiridos para identificar a sua estrutura no interior do óxido. Ainda, observaram-se bolhas na superfície do eletrodo superior dos dispositivos com difusão de vacâncias de oxigênio após o tratamento elétrico. Nesse mesmo contexto, foi medida a difusividade e energia de ativação da difusão de oxigênio em filmes finos de TiOy. / In this work we developed a systematic study of diffusion mechanisms which are responsible for resistance switching in resistive memories. The structure of these memories is similar to a capacitor which suffers resistance transition induced by electrical field. The transition is caused by the formation of conductive filaments inside the semiconductor matrix. The filaments may be constituted by metal from one of the electrodes (ECM) or by oxygen deficient areas (VCM), generated from oxygen vacancies diffusion. Devices of TiO2 have been built and its electrical response was acquired through electrical measurements (I-V) for different electrode metals. Ion beam techniques such as micro-probe Rutherford Backscattering and Nuclear Reaction Profiling were used to detail the diffusion processes. It was observed a dependence in the electrical behaviour with the semiconductor layer deposition method, its thickness and bias measurement parameters. In the case which filaments are composed by metal atoms, measurements of micro-RBS were performed to identify its structure inside the oxide. Also, bubbles have been observed over the surface of top electrode in devices with oxygen vacancies diffusion after the electrical treatment. In this context, it was measured diffusivity and activation energy for oxygen diffusion in thin TiOy films.

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2015-03-03T10:53:35Z No. of bitstreams: 0 / Made available in DSpace on 2015-03-03T10:53:35Z (GMT). No. of bitstreams: 0 / Tese (Doutorado em Tecnologia Nuclear) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Neste trabalho foi desenvolvido um estudo sistemático dos mecanismos de difusão responsáveis pelo switching de resistência em memórias resistivas. Essas memórias possuem estrutura semelhante a de um capacitor, a qual sofre uma transição de resistência induzida pela aplicação de um campo elétrico. A transição é provocada pela formação de filamentos condutivos no interior da matriz semicondutora. Os filamentos podem ser constituídos por metal originado de um dos eletrodos (ECM) ou por regiões do óxido deficientes em oxigênio (VCM), geradas pela difusão de vacâncias de oxigênio. Dispositivos de TiO2 foram construídos e sua resposta elétrica foi adquirida através de medidas elétricas do tipo I-V para diferentes metais de eletrodo. Técnicas de análise por feixe de íons, como retroespalhamento Rutherford por micro-feixe e perfilometria com reação nuclear ressonante, foram usadas para detalhamento dos processos de difusão. Constatou-se uma dependência do comportamento elétrico em função do método de deposição da camada semicondutora, sua espessura e os parâmetros da medida de tensão. No caso do filamento ser composto por átomos de metal, espectros de micro-RBS foram adquiridos para identificar a sua estrutura no interior do óxido. Ainda, observaram-se bolhas na superfície do eletrodo superior dos dispositivos com difusão de vacâncias de oxigênio após o tratamento elétrico. Nesse mesmo contexto, foi medida a difusividade e energia de ativação da difusão de oxigênio em filmes finos de TiOy. / In this work we developed a systematic study of diffusion mechanisms which are responsible for resistance switching in resistive memories. The structure of these memories is similar to a capacitor which suffers resistance transition induced by electrical field. The transition is caused by the formation of conductive filaments inside the semiconductor matrix. The filaments may be constituted by metal from one of the electrodes (ECM) or by oxygen deficient areas (VCM), generated from oxygen vacancies diffusion. Devices of TiO2 have been built and its electrical response was acquired through electrical measurements (I-V) for different electrode metals. Ion beam techniques such as micro-probe Rutherford Backscattering and Nuclear Reaction Profiling were used to detail the diffusion processes. It was observed a dependence in the electrical behaviour with the semiconductor layer deposition method, its thickness and bias measurement parameters. In the case which filaments are composed by metal atoms, measurements of micro-RBS were performed to identify its structure inside the oxide. Also, bubbles have been observed over the surface of top electrode in devices with oxygen vacancies diffusion after the electrical treatment. In this context, it was measured diffusivity and activation energy for oxygen diffusion in thin TiOy films.

Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2015-03-03T10:53:35Z No. of bitstreams: 0 / Made available in DSpace on 2015-03-03T10:53:35Z (GMT). No. of bitstreams: 0 / Resíduos da área de engenharia civil decorrentes da recuperação de estruturas danificadas por agentes agressivos contribuem continuadamente para impactar o meio ambiente de maneira cada vez mais preocupante. O desenvolvimento de novas tecnologias que sejam aceitáveis do ponto de vista ambiental e financeiro provou ser um grande desafio na solução desse problema quando se compara o custo original e eficaz em médio e longo prazo ao custo da demolição, destinação desse material e reconstrução da obra. Para viabilizar a utilização de compósitos de fibras sintéticas como reforço resistente a ambientes agressivos em elementos de concreto, os aparatos de ensaio e os corpos de prova foram modificados e adaptados aos sistemas operacionais descritos pelas normas técnicas vigentes, a partir da concepção do uso de filamentos de fibra contínua. Dado o caráter inovador do trabalho, não se identificou uma norma que tratasse especificamente dos ensaios de flexão nem pullout com fibras contínuas em blocos de concreto. Portanto, para se conseguir um aproveitamento desse tipo de reforço que respondesse satisfatoriamente quando comparado às armaduras metálicas, foi aplicada uma rugosidade à superfície da haste para garantir sua aderência ao bloco de concreto. Pelo método de preparo de compósitos de matriz cimentícia proposto no presente estudo, foram determinados os valores da força de arrancamento dos reforços com fibras de carbono e vidro-AR, os quais, no caso das fibras de carbono, apresentaram aumentos significativos entre 76% e 158% e 47% e 120% respectivamente para concretos de resistência à compressão de 30 MPa (fcm 30) e 40 MPa (fcm 40) comparados com valores obtidos para barras de aço. / Tese (Doutorado em Tecnologia Nuclear) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

No description available.

Les divisions méiotiques sont très asymétriques en taille et génèrent une très grosse cellule, l'ovocyte, et deux petites cellules, les globules polaires. Cette asymétrie est permise par la migration du fuseau lors de la première division jusqu'au cortex le plus proche. Cette migration ne dépend pas des microbutules mais de la Myosin-II et d'un réseau de filaments d'actine nucléé par la coopération des nucléateurs de filaments droits Formin-2 et Spire1/2. Des observations préliminaires effectuées au laboratoire ont décrit un épaississement du cortex d'actine pendant la migration du fuseau, mais pourtant il avait été montré que la tension corticale, un paramètre décrivant la rigidité de l'ovocyte, diminue pendant la migration du fuseau. J'ai montré que cet épaississement est indispensable à la migration du fuseau et est nucléé par le nucléateur de filaments branchés Arp2/3, sous le contrôle de la voie Mos/MAPK. De plus, il provoque la diminution de la tension corticale en délocalisant la Myosin-II, ce qui est indispensable à la migration du fuseau. Finalement, j'ai montré que le chute de tension est un mécanisme d'amplification du déséquilibre des forces présent initialement (grâce au léger décentrage du noyau) qui déclenche la migration du fuseau. / Meiotic divisions are highly asymmetric divisions in size, generating a big cell, the oocyte, and two tiny cells, the polar bodies. This asymmetry is ensured by the migration of the first meiotic spindle to the closest cortex. This migration does not depend on microtubules but on Myosin-II and an F-actin meshwork nucleated by cooperation of straight filament nucleators Formin-2 and Spire1/2. Preliminary studies in the lab described a thickening of the F-actin cortex during spindle migration, but paradoxically cortical tension, a physical parameter describing the stiffness of the cell, drops during spindle migration. I have shown that this thickening is required for spindle migration and nucleated by the branched actin nucleator Arp2/3, under the control of the Mos/MAPK pathway. Furthermore, it promotes the decrease in cortical tension by triggering the delocalization of Myosin-II from the oocyte cortex, which is crucial for spindle migration. Finally, I have shown that the drop in cortical tension is an amplificatory mechanism to the initial unbalance of forces (due to a slight off-centered position of the nucleus) triggering the motion of the spindle.

Hautement conservé, de la bactérie jusqu'à l’Homme, la recombinaison homologue est indispensable à la survie de tout organisme vivant. Chez l’humain, la protéine hRad51 (human Rad51) y joue un rôle clé en s’autoassemblant au site de cassure sur les extrémités simple-brin d’une molécule d’ADN endommagée pour former le filament nucléoprotéique. Ce filament est capable à lui seul d’effectuer la plupart des opérations nécessaires au bon déroulement de la recombinaison homologue; il va permettre la reconnaissance d’homologie, l’appariement des séquences homologues et l’invasion de brins requise pour la synthèse de l’ADN manquant.La recombinaison homologue est un processus complexe impliquant de multiples partenaires. Pour mieux comprendre le rôle du filament nucléoprotéique au sein de la réaction, on se propose d’étudier ce dernier en l’absence de tout partenaire. Plus précisément, on observe le comportement mécanique de filaments hRad51-ADNdb en fonction des conditions chimiques. La formation du filament nucléoprotéique modifie la conformation de l’ADN sur lequel il s’assemble, l’allongeant de 50% et le déroulant de 43% dans le cas d’une molécule double-brin. Les pinces magnétiques sont un outil permettant de contrôler la force et la torsion appliquées à une unique molécule d’ADN double-brin (ADNdb), elles sont donc l’outil idéal pour sonder les propriétés mécaniques de filaments nucléoprotéiques. Le système des pinces magnétiques a été modifié afin de mesurer des paramètres mécaniques précédemment inaccessibles tel que le couple ressenti ou exercé par le filament. Le but de cette thèse a été d’étudier les propriétés mécano-chimiques des filaments nucléoprotéiques tout en essayant de tracer le paysage énergétique qui régit les transitions de ces systèmes. / Highly conserved throughout the species, homologous recombination is crucial to the survival of any living organism. In humans, the hRad51 protein (human Rad51) plays a key role by self-assembling at the break site on the single stranded extremities of damaged DNA molecules thus forming the nucleoprotein filament. This filament is able by itself to accomplish most of the necessary operations of homologous recombination; it allows the homology search, the pairing of the homologous sequences and the strand exchange.Homologous recombination is a complex process involving many partners. In order to better understand the role of the nucleoprotein filament in this process, we propose to study it in the absence of any partners. We will focus on the study of the mechanical properties of hRad51-dsDNA filaments as a function of chemical conditions. The formation of the nucleoprotein filament modifies the conformation of the DNA molecule on which it assembles, stretching it by 50% and unwinding it by 43% in the case of a double stranded DNA. The magnetic tweezers are a tool allowing the control of the force and torsion applied to a single dsDNA molecule; they are therefore the ideal tool to probe the mechanical properties of nucleoprotein filaments. We modified the magnetic tweezers as to allow the measurement of previously inaccessible mechanical parameters such as the torque applied or felt by the filament. The goal of this thesis has been to study the mechano-chemical properties of nucleoprotein filaments while drawing the energy landscape that governs the various transitions of these systems.

No description available.

Cells grow in environments that can change suddenly. To cope with unpredictable perturbations, they have evolved mechanisms to adjust their metabolism according to the various types of environmental stress. Cells experiencing starvation, for example, have low energy levels and are forced to lower their metabolism and enter a protective quiescent state to survive until nutrients become available again. Recently, it has been shown that starved yeast cells experience a marked acidification of the cytoplasm, due to a passive influx of protons. This pH drop causes multiple rearrangements in the cytoplasm: increased crowding, reduced mobility of intracellular components and formation of stress-induced non-membrane bound compartments of specific metabolic enzymes. Cytoplasm rearrangements are required for cell survival and can be reversed upon replenishment of energy. However, there is little understanding of how cytoplasmic components reorganize in stressed quiescent cells. Using high-pressure freezing, correlative light and electron microscopy (CLEM) and electron tomography, coupled to high-resolution 3D-reconstruction techniques, I investigate the structural modi cations that happen in situ in yeast cells undergoing quiescence. I observe that the cytoplasm becomes increasingly crowded, due to a massive rearrangement of membranous structures, including accumulation of intracellular vesicles and pronounced invaginations in the plasma membrane. This is proved by quantification of the difference in ribosome densities between stressed and not stressed cells. The increased crowding, coupled to cytoplasm acidification, leads to the formation of non-membrane bound enzyme compartments, that appear as foci and elongated structures of fluorescently tagged enzymes. I prove that the fluorescent structures correspond to bundles of filaments. Among many essential enzymes, known to form mesoscale structure in stressed yeast, I demonstrate that the eukaryotic translation initiation factor 2B (eIF2B) forms bundles of filaments in situ, and the evolutionary conserved glutamine synthetase (Gln1) self-assembles into filaments in vitro. The present study on the energy depleted cytoplasm and the structural analysis of filament-forming enzymes provides insights into an unexplored survival strategy that is used by yeast, as well as other organisms, to cope with extreme environmental conditions and stress.:1 Introduction 1 Stress, survival and quiescence 2 1.1 Cytoplasm and cellular compartments 2 1.2 Membraneless compartmentalization in the cell 3 1.3 Stress-induced non-membrane bound assemblies 4 The quiescent sleeping yeast 6 1.4 The yeast S.cerevisiae as model organism 7 1.5 Growth and metabolism of yeast 9 1.5.1 Yeast eukaryotic translation initiation factor 2B: eIF2B 11 1.5.2 Yeast glutamine synthetase: Gln1 12 3D electron microscopy 14 Aims of the Thesis 18 2 Materials and methods 21 Room temperature electron microscopy (EM) 21 2.1 Yeast strains, media and energy depletion 21 2.2 High-pressure freezing of yeast cells 22 2.2.1 EM sample preparation for untagged eIF2B yeast strains 22 2.2.2 EM sample preparation for GFP-tagged eIF2B yeast strains 23 2.3 Electron tomography 23 2.4 Subtomogram averaging 24 2.5 Fiji script for automated ribosome counting 25 2.6 Immunofluorescence of eIF2B in yeast 26 2.7 Western-blot on yeast ribosomes 27 Single particle procedures 30 2.8 Protein purification protocols 30 2.8.1 Baculovirus-insect cell expression and purification of eIF2B 30 2.8.2 Gradient of fixation for fragile complexes 31 2.8.3 Yeast expression and purification of Gln1 33 2.9 Negative staining 34 2.9.1 Image acquisition and analysis—eIF2B 35 2.9.2 Image acquisition and analysis—Gln1 36 Cryo-electronmicroscopy(cryo-EM) 37 2.10 Plunge freezing 37 2.11 Image acquisition and 3D reconstruction 37 3 Results Visualizing yeast’s cytoplasmic reorganization 39 3.1 Quiescence is accompanied by reorganization of the cytoplasm 40 3.2 Ribosome density proves cytoplasmic crowding in starved cells 42 3.3 eIF2B organizes in bundles of filaments in energy-depleted cells 45 3.4 eIF2B filaments are polymers of the eIF2B complex 47 3.5 Filaments are found in wild-type energy-depleted cells 49 Structural analysis of filament forming enzymes 51 3.6 Purification of eIF2B complexes 51 3.7 Single particle analysis of eIF2B 53 3.8 Purification of Gln1 complexes 55 3.9 Single particle analysis of Gln1 56 3.10 Gln1 forms filaments in vitro 58 4 Discussion and Outlook 59 4.1 Yeast cytoplasm reorganizes in response of stress 59 4.2 Ribosomes density is a measure of increased macromolecular crowding 60 4.3 eIF2B forms filaments as a survival strategy 62 4.4 Molecular analysis of filament forming enzymes 64 4.5 Outlook 65 Appendix 67 Bibliography 83

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18285号 / 工博第3877号 / 新制||工||1595(附属図書館) / 31143 / 京都大学大学院工学研究科電子工学専攻 / (主査)教授 木本 恒暢, 教授 藤田 静雄, 准教授 掛谷 一弘 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM