Dissertations / Theses: 'STM1'

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Ilina, Yulia. "Functions of the yeast protein Stm1 and its involvement in apoptotic cell death." [S.l. : s.n.], 2005.

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Balagopal, Vidya. "STM1 IS A NOVEL REGULATOR OF MESSENGER RNA TRANSLATION AND DEGRADATION IN SACCHAROMYCES CEREVISIAE." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/145717.

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In eukaryotes, regulation of translation and decay of messenger RNA are critical for fine-tuned control of gene expression. An important point of control is the key transition where mRNAs exit translation and assemble into a non-translating mRNP state that can accumulate in cytoplasmic granules such as P bodies and/or Stress granules. In the budding yeast Saccharomyces cerevisiae , the activators of decapping Dhh1 and Pat1 appear to promote the exit of mRNAs from translation. In my work, summarized below, I describe a new regulator of translation repression and mRNA degradation, Stm1, and its novel mode of action. First, I identified Stm1 as a novel regulator of translation repression and mRNA decay. Stm1 shows several genetic interactions with Pat1 and Dhh1, in a manner consistent with Stm1 promoting the function of Dhh1. This suggests that Stm1 has a role to play in translation repression and/or activation of mRNA decay. stm1 δ strains are defective in the degradation of a subset of mRNAs that include EDC1 and COX17 . These results strongly argue that Stm1 is a novel addition to the mRNA degradation machinery. Second, I have shown that Stm1, a known ribosome-associated protein, can bind and stall 80S ribosomes to repress translation and promote decay. Stm1 is able to repress translation and stall an 80S complex in vitro . Several mutations were identified in the protein, which link the in vitrophenotype to its biological functionin vivo. The analysis of different steps in translation reveals Stm1 functions in a novel manner to inhibit translation after the formation of an 80S complex. Since most of the regulation of translation is thought to happen at the stage of initiation, this study reveals a novel mode of translation regulation. These results also provide a direct and mechanistic link between ribosome function, inhibition of translation and the degradation of messenger RNAs.

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Gatsos, Xenia, and xgatsos@optusnet com au. "The development of live vectored vaccines targeting the alpha-toxin of Clostridium perfringens for the prevention of necrotic enteritis in poultry." RMIT University. Applied Sciences, 2007. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20080212.142403.

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The Ñ-toxin of Clostridium perfringens is a toxin involved in numerous diseases of humans and agriculturally important animals. One of these diseases is necrotic enteritis (NE), a sporadic enteric disease which affects avian species world-wide. This study involved the inactivation of alpha-toxin (Ñ-toxin) for use as a potential vaccine candidate to combat NE in chickens, and other diseases caused by C. perfringens type A. During the course of this research a number of Ñ-toxin recombinant proteins were developed through molecular inactivation of the Ñ-toxin gene, plc. Proteins plc316 and plc204 were developed by the deletion of the first three and seven Ñ-helices of the N-terminal domain respectively. These deletions resulted in proteins which were unstable in solution, constantly aggregated into insoluble masses and elicited lower overall antibody responses when administered to mice. A third protein, plcInv3 was developed from the deletion of part of the catalytic domain of the Ñ-toxin. PlcInv3 was highly soluble and upon immunisation of mice elicited a significant antibody response which was also capable of protecting mice against a live challenge of C. perfringens. The fourth and final protein developed was plc104. The smallest of the recombinant Ñ-toxin proteins, it consisted entirely of the C-terminal domain of Ñ-toxin. Its small size did not affect its ability to induce a strong antibody response when administered to mice, the antibodies of which were also protective during a challenge with C. perfringens. STM1, an attenuated strain of S. Typhimurium was used in the development of a vectored vaccine for the expression and oral delivery of plcInv3 and plc104 within the mouse host. The proteins were expressed within STM1 from expression plasmids containing the in vivo inducible promoters PhtrA and PpagC. A measurable humoral immune response against Ñ-toxin was absent following three oral vaccinations with the vectored vaccines, although, cytokine profiling of splenocytes from vaccinated mice revealed an increase in the number of interleukin-4 (IL-4)secreting cells and the lack of interferon-gamma (IFN-×) secreting cells. This indicated the stimulation of a T-helper type 2 (TH2) immune response which also lead to partial protection against a live C. perfringens challenge. This study demonstrates the feasibility of using STM1 as a carrier for the in vivo expression of the C. perfringens Ñ-toxin recombinant proteins plcInv3 and plc104. It is the first study to express C. perfringens antigens within an attenuated strain of S. Typhimurium, STM1.The partial protection of mice immunised with these vaccines indicates there is potential for this vectored vaccine system to be used in the protection of diseases caused by the Ñ-toxin of C. perfringens.

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ABREU, FERNANDA DE MELLO. "TIME-DOMAIN OPTICAL MULTIPLEXING IN STM-16, STM-64 AND STM-256 SYSTEMS." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2001. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=2361@1.

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PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO
ALCATEL TELECOMUNICAÇÕES
Este trabalho tem como foco o up-grade da taxa de bits em enlaces ópticos através da tecnologia OTDM. Os sistemas analisados contemplam os up-grades das taxas de 2,48 Gbps para 10 Gbps e também da taxa de 10 Gbps para 40 Gbps. Para tal, foram introduzidos módulos de transmissão e recepção, capazes de utilizar arquiteturas quase totalmente ópticas. É avaliado então, através de simulações, o comportamento da arquitetura proposta em infra-estruturas de enlaces já instalados no Brasil, destacando os pontos mais críticos. No que se refere ao up-grade de 10 Gbps para 40 Gbps, foi dado enfoque especial para as penalidades relativas à PMD (Polarization Mode Dispersion).
This work aims at up grading the bit rate of optical links through the OTDM technology. The analyzed up-grades change the bit rate of 2,48 Gbps up to 10 Gbps and also from the bit rate of 10 Gbps up to 40 Gbps. To reach these objectives, transmission and reception modules were introduced, using all optical networks topologies. The performance of the proposed architecture was simulated using a infrastructure of links already installed in Brazil. The most critical issues were pointed out. Concerning the up-grade from 10 Gbps to 40 Gbps, a special focus was given to the penalties due to PMD (Polarization Mode Dispersion).

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Al, Badine Samir. "STMM soumission de travaux en mode messagerie /." Grenoble 2 : ANRT, 1988. http://catalogue.bnf.fr/ark:/12148/cb37611499t.

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Lampe, Birgit [Verfasser]. "Transkranielle Einzelimpulsstimulation (sTMS) bei akustischer Verbgenerierung / Birgit Lampe." Köln : Deutsche Zentralbibliothek für Medizin, 2012. http://d-nb.info/1024715361/34.

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Cardoso, Aline Monticelli 1988. "Estudos sobre a internalização celular da STC1 humana." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314360.

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Orientador: Jörg Kobarg
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A Stanniocalcina-1 (STC1) humana é uma glicoproteína homóloga a Stanniocalcina (STC) originalmente identificada como um hormônio regulador da homeostase de cálcio em peixes. A STC1 humana secretada atua em diferentes processos fisiológicos incluindo a angiogênese, a hipóxia e, principalmente, a carcinogênese, demonstrando assim uma atividade abrangente. Atualmente não se conhece o receptor da STC1 e pouco se sabe sobre o mecanismo de ação e de entrada nas células dessa proteína. Assim, o objetivo desse trabalho foi investigar um candidato a receptor de membrana dessa proteína, o receptor de transferrina (TfR1), uma proteína transmembrana responsável pela absorção de ferro nas células. Esse receptor é provavelmente expresso por todas as células em diferentes níveis, em destaque em células do sistema hematopoiético, em células em divisão celular e células neoplásicas. Assim, avaliou-se por citometria de fluxo o efeito do tratamento com STC1 em células não transfectadas e células transfectadas superexpressando o receptor de transferrina. Células tratadas com STC1 demonstraram um efeito semelhante ao tratamento com transferrina, um conhecido ligante desse receptor, no qual ambos diminuíram o número de células positivas para a marcação da superfície com transferrina conjugada com fluorocromo (transferrina-Alexa Fluor® 488 - Life Technologies). Em outro conjunto de experimentos de Western Blot foi demonstrado que a STC1 adicionada no sobrenadante das culturas de células é internalizada nas células e detectável no lisado celular, principalmente as células transfectadas para a superexpressão do receptor de transferrina. Complementarmente, em experimentos de localização subcelular por imunofluorescência a STC1 foi detectada em uma forma pontual e espalhada no citoplasma. Em conjunto, todos esses experimentos sugerem que STC1 e transferrina interferem na localização do receptor de transferrina na superfície celular e que possivelmente esse receptor está envolvido em mecanismos de internalização da própria STC1
Abstract: Human Stanniocalcin 1 (STC1) is the mammalian homologue of STC, which was originally identified as a calcium-regulating hormone in bony fishes. The human secreted Stanniocalcin acts on different physiological processes, including angiogenesis, hypoxia and especially carcinogenesis, facts that demonstrate their activity is wide. Currently there are few data on the mechanism of action of this protein or how it enters the cell. Thus, the aim of this study was to investigate transferrin receptor (TfR1) as a candidate to membrane receptor protein of STC1. This receptor is a membrane protein responsible for the iron uptake in cells. This receptor is probably expressed by all cells especially by cells in division and cancer cells, but its expression level may vary. We evaluated by flow cytometry the effect of STC1 treatment in non-transfected cells and cell with TfR1 overexpression. The treatment with STC demonstrated a similar effect to treatment with transferrin, a known ligand for receptor, which decreased the number of positive cells for staining with fluorochrome (transferrin conjugated to Alexa Fluor® 488 - Life Technologies). We also demonstrated by Western Blot that STC1 added to the supernatant of cultures of cells, especially cells that overexpress transferrin receptor, is internalized into the cells and detectable in the cell lysate. Additionally, in subcellular localization experiments by immunofluorescence STC1 was detected in a timely manner and scattered in the cytoplasm. Together all this information suggests that STC1 and transferrin interferes with the localization of the transferrin receptor in the cellular surface and perhaps this receptor is involved in the mechanism of internalization of STC1
Mestrado
Bioquimica
Mestra em Biologia Funcional e Molecular

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Holl, Christian [Verfasser], Markus [Akademischer Betreuer] Morgenstern, and Samir [Akademischer Betreuer] Lounis. "High frequency STM and spin polarized STM on magnetic vortices / Christian Holl ; Markus Morgenstern, Samir Lounis." Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://d-nb.info/1192217926/34.

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Azevedo, Cristina Maria LourencÌ§o da Cunha Correia de. "Functional analysis of RAR1 and STG1 in disease resistance." Thesis, University of East Anglia, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399785.

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Troupes, Constantine. "The Role of STIM1 in Hypertrophy-Related Contractile Dysfunction." Diss., Temple University Libraries, 2016. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/403786.

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Biomedical Sciences
Ph.D.
Increases in cardiac afterload caused by disease conditions results in remodeling of heart structure by hypertrophy and alterations in the molecular regulation of contractile performance. These adaptations can be regulated by various Ca2+-dependent signaling processes. STIM1 is an important regulator of Ca2+ signaling in different cell types by sensing endoplasmic reticular Ca2+ levels and coupling to plasma membrane Orai channels. The role of STIM1 in heart is not well understood, given the robust Ca2+ regulatory machinery present within cardiac myocytes. Previous reports indicate that STIM1 may play a role in regulation of cardiac hypertrophy. The goal of this work is to understand how STIM1 can affect contractile Ca2+ regulation in normal and diseased myocytes. We induced cardiac hypertrophy by slow progressive pressure overload in adult cats. Isolated adult feline ventricular myocytes (AFMs) exhibited increased STIM1 expression and activity, which correlated with altered Ca2+ handling. Use of BTP2 to block Orai channels resulted in a reduction of action potential (AP) duration and diastolic spark rate of hypertrophied myocytes, without affecting myocytes from sham-operated animals. Overexpressed STIM1 in cultured AFMs caused persistent Ca2+ influx that resulted in increased diastolic spark rates and prolonged APs, similar to myocytes from banded animals. STIM1 mediated Ca2+ influx could load the sarcoplasmic reticulum and activated CaMKII, which increased spark rates and lead to spontaneous APs. Importantly, STIM1 operated by associating with Orai channels because these effects could be blocked with either BTP2 or with a dominant negative Orai construct. Prolonged Ca2+ entry through this pathway eventually causes cell death. In conclusion, the work presented in this thesis establishes a role for STIM1-Orai in contractile Ca2+ regulation.
Temple University--Theses

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Walsh, Ciara. "The regulation of STIM1 translocation to the plasma membrane." Thesis, University of Liverpool, 2010. http://livrepository.liverpool.ac.uk/1482/.

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A rise in intracellular Ca2+ concentration is key to controlling both short term and long term Ca2+ dependent processes which include secretion, metabolism and gene expression, cell growth and proliferation. Store operated Ca2+ channels (SOCs), which are activated by the depletion of Ca2+ from internal Ca2+ stores, the main store being the endoplasmic reticulum (ER), are the major route for Ca2+ influx in non-excitable cell types. Stromal interacting molecule 1 (STIM1) is a Ca2+ sensing protein located in the endoplasmic reticulum (ER). Depletion of ER calcium stores triggers oligomerisation and subsequent translocation of STIM1 from its reticular location to specialized endoplasmic reticulum-plasma membrane (ER-PM) junctions where it forms STIM1 puncta and interacts with the SOC channel, Orai1. This induces the clustering of Orai1 into a functional tetrameric pore which is permeable to Ca2+ ions, enabling Ca2+ entry into the cell. The precise mechanism by which STIM1 is recruited to the plasma membrane to activate SOCs and the plasma membrane components involved in targeting STIM1 to the plasma membrane are largely unknown. In this study the mechanisms underlying movement of STIM1 to the plasma membrane and its accumulation at ER-plasma membrane junctions was explored in HeLa cells. In the initial part of this study I investigated whether the movement of STIM1 to the plasma membrane is an ATP-dependent process. I found that depletion of cytosolic ATP can stimulate STIM1 puncta formation in HeLa cells and that the formation of STIM1-Orai1 complexes at the plasma membrane is unaffected in these conditions. Inhibition of ATP synthesis also initiated the loss of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) from the plasma membrane. ATP depletion did not affect the structure of the microtubule cytoskeleton. These results suggest that the translocation of STIM1 and the formation of STIM1-Orai1 complexes is an ATP independent process which is not due to the disruption of microtubules and support a diffusional model for STIM1 puncta formation. It has been suggested that an additional interaction of the C-terminal polybasic domain of STIM1 with plasma membrane phosphoinositides could contribute to STIM1 puncta formation prior to binding to Orai1. I investigated the role of phosphoinositides in the formation of STIM1 puncta and SOCE in response to store depletion. Treatment of HeLa cells with inhibitors of the phosphatidylinositol 3-kinase (PI3K) and phosphatidylinositol 4-kinase (wortmannin and LY294002) partially inhibited formation of STIM1 puncta. Additional rapid depletion of PtdIns(4,5)P2 resulted in more substantial inhibition of the translocation of STIM1-EYFP into puncta. The inhibition was extensive at a concentration of LY294002 (50 μM) that should primarily inhibit PI3K consistent with a major role for PtdIns(4,5)P2 and PtdIns(3,4,5)P3 in puncta formation. Depletion of phosphoinositides also partially inhibited SOCE. Overexpression of Orai1 resulted in a recovery of translocation of STMI1 into puncta following phosphoinositide depletion and under these conditions SOCE was increased to above control levels. These observations support the idea that phosphoinositides are not essential but contribute to STIM1 accumulation at ER-PM junctions with a second translocation mechanism involving direct STIM1/Orai1 interactions. It was recently reported that STIM1 and Orai1 may function within a macromolecular complex involving other unidentified proteins. In this study I have identified that Golli-BG21, a member of the myelin basic protein (MBP) family, can directly interact with STIM1. Golli interacts with the C-terminal domain of STIM1 in both in vitro and in vivo binding assays and this interaction may be modulated by intracellular Ca2+ concentration. Golli also colocalises with full length STIM1 and Orai1 complexes in HeLa cells following store depletion. Overexpression of Golli reduces SOCE in HeLa cells but this inhibition is overcome by overexpressing STIM1. We therefore suggest that Golli binds to STIM1-Orai1 complexes to negatively regulate the activity of SOCs.

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Wiehlmann, Lutz. "Sequenzspezifizierte Transposonmutagenese (STM) in Pseudomonas aeruginosa." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=96511211X.

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13

Ruess, Frank Joachim Physics Faculty of Science UNSW. "Atomically controlled device fabrication using STM." Awarded by:University of New South Wales. Physics, 2006. http://handle.unsw.edu.au/1959.4/24855.

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We present the development of a novel, UHV-compatible device fabrication strategy for the realisation of nano- and atomic-scale devices in silicon by harnessing the atomic-resolution capability of a scanning tunnelling microscope (STM). We develop etched registration markers in the silicon substrate in combination with a custom-designed STM/ molecular beam epitaxy system (MBE) to solve one of the key problems in STM device fabrication ??? connecting devices, fabricated in UHV, to the outside world. Using hydrogen-based STM lithography in combination with phosphine, as a dopant source, and silicon MBE, we then go on to fabricate several planar Si:P devices on one chip, including control devices that demonstrate the efficiency of each stage of the fabrication process. We demonstrate that we can perform four terminal magnetoconductance measurements at cryogenic temperatures after ex-situ alignment of metal contacts to the buried device. Using this process, we demonstrate the lateral confinement of P dopants in a delta-doped plane to a line of width 90nm; and observe the cross-over from 2D to 1D magnetotransport. These measurements enable us to extract the wire width which is in excellent agreement with STM images of the patterned wire. We then create STM-patterned Si:P wires with widths from 90nm to 8nm that show ohmic conduction and low resistivities of 1 to 20 micro Ohm-cm respectively ??? some of the highest conductivity wires reported in silicon. We study the dominant scattering mechanisms in the wires and find that temperature-dependent magnetoconductance can be described by a combination of both 1D weak localisation and 1D electron-electron interaction theories with a potential crossover to strong localisation at lower temperatures. We present results from STM-patterned tunnel junctions with gap sizes of 50nm and 17nm exhibiting clean, non-linear characteristics. We also present preliminary conductance results from a 70nm long and 90nm wide dot between source-drain leads which show evidence of Coulomb blockade behaviour. The thesis demonstrates the viability of using STM lithography to make devices in silicon down to atomic-scale dimensions. In particular, we show the enormous potential of this technology to directly correlate images of the doped regions with ex-situ electrical device characteristics.

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Deshpande, Aparna. "Atomistic interactions in STM atom manipulation." Ohio : Ohio University, 2007. http://www.ohiolink.edu/etd/view.cgi?ohiou169849272.

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Dixon, Richard. "STM studies of semiconducting metal oxides." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365728.

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Revenikiotis, Sackis (Athanasios). "Optimization of STM-tip preparation methods." Thesis, KTH, Materialfysik, MF (Stängd 20120101), 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-30873.

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The Scanning Tunneling Microscope (STM) was invented by Gerd Binnig and Heinrich Rohrer and gave them the Nobel Prize in Physics 1986. STM can give us atomic resolution of a surface by applying a voltage between a very sharp tip (STM-tip) and the surface of a material that we want to examine. The STM-tip is moving over the surface and a computer is collecting the tunnel current in every single point to create a digital image. This diploma work is focused on the preparation of the STM-tip. The preparation method that is used is electrochemical etching of a tungsten wire. The sharper the STM-tip is the better resolution in the STM images we can get. With the purpose to get as sharp tip as possible and with a well-defined geometry, we prepared several tips by systematically varying the etching parameters such as voltage, current, concentration and wire length. A new method has been tested to minimize the oxidation on the surface and finally the tips were characterized with scanning electron microscope (SEM).

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Wilson, Jon H. "Silicon surfaces : STM, theory and experiment." Thesis, University of Oxford, 1991. http://ora.ox.ac.uk/objects/uuid:64998ae3-9316-42b5-967f-da93ff2bfd6c.

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The fundamental atomic and electronic behaviour of clean silicon surfaces has been studied within a simple tight-binding picture of bonding in solids. Of the various contributions to the surface binding energy, the lowering in the promotion energy (i.e. rehybridization) which accompanies localized Jahn-Teller distortions has been identified as a major electronic driving force underlying the stability of silicon surfaces. The structure of Si(113) has been experimentally determined by the technique of scanning tunnelling microscopy (STM). Despite its high index, the Si(113) surface is found to be highly stable. STM images of both empty and filled states provide strong evidence for a particular structural model with a 3x2 unit cell. The STM results are explained in terms of a general rehybridization principle, suggested by the earlier theoretical study, which accounts for the low surface energy as well as the observed spatial distribution of empty and filled states. In addition, the STM images reveal a high density of domain boundaries which introduce energy states that pin the Fermi level and explain earlier reports of a 3x1 reconstruction for this surface. Voltage-dependent STM image simulations for the Si(113)3x2 surface have been carried out using a simple tight-binding description of surface electronic structure. Quantitative agreement with experiment is obtained confirming the qualitative rehybridization arguments used previously. The local barrier for tunnelling electrons is shown to have an important effect on the interpretation of STM images. The high stability of clean Si(l 13) is shown by STM to be disrupted by adsorption of submonolayer amounts of atomic hydrogen which saturates dangling bonds. Mass transport of silicon occurs and structural models are proposed for the resultant mixed 2x2 and 2x3 surface.

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Clarke, A. R. H. "Quantitative STM imaging of metal surfaces." Thesis, University of Oxford, 1996. http://ora.ox.ac.uk/objects/uuid:68cbeba7-d283-498a-9435-b9587e7ef30a.

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Many deductions made about STM images are based upon the model of Tersoff and Hamann, in which images are given in principal by a combination of surface atomic positions and local charge density. There is a now a need for a fuller understanding of this technique in order to explain experimental evidence which indicates that the tip and sample can interact strongly during normal imaging. In order to investigate the fundamental STM imaging process, a method for deducing the tunnel barrier height has been developed which is based on corrugation height measurements of constant current topographs. From experiments on clean Cu(100), values of the tunnel barrier height have been shown to be somewhat below the workfunction (~ 1-2.5eV) but are in good agreement with other reports of atomically resolved barrier height data. At large values of the tunnel conductance (~ 1μS), a fall-off (based upon extrapolation of large separation data) in the corrugation heights is observed with increasing conductance. This effect is quantitatively explained using a Molecular Dynamics simulation of the tip approaching the sample. The simulation gives a good estimate of both the absolute tip-sample separation and site-dependent tip-surface forces. Distributions of corrugation heights indicate that variations in both tip geometry and chemistry are likely to occur in practice and strongly influence the phenomena described above. Similarly, it is found that increased local tunnel barrier heights are measured when the Cu(100) surface is modified with small numbers of single halogen atoms. This data has been used to estimate the contributions to the increase in local barrier height of both adsorbate induced dipoles and geometric topography. Values for the charge transfer between the surface and adsorbate have been established. The process of tip-induced adsorbate manipulation has also been demonstrated at room temperature.

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Silva, Neto Francisco Miranda Soares da. "Rewriting Concurrent Haskell programs to STM." Universidade Federal de Pernambuco, 2014. https://repositorio.ufpe.br/handle/123456789/11435.

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In recent years, the diminishing rate with which we can increase the amount of transistors in a processor core has slowed down the increase of computers’ power. Moore’s Law appears to be drawing to an end. With it, the assumption that software written today will be more efficiently executed in the future simply due to processors’ evolution is being challenged. On the other hand, parallel applications can still be made more efficient by distributing work among different processors to be executed at the same time, thus reducing overall execution time. To enable parallelization, we must have multiple processor cores. This has led to the popularization of multicore architectures. However, writing parallel applications is not trivial. A program must be either written from the start to be executed in parallel, or later adapted for parallel execution. The programmer has the error-prone task of parallelizing the application through use of concurrency and parallelism constructs. Locking, the most common concurrency option, presents risks for inexperienced programmers, such as the famous Deadlock and Livelock problems. As we move from single core architectures to multicore, our programming languages need to make it easier for the programmers to use concurrency. Many researchers have pointed at Software Transactional Memory (STM) as an answer to that issue, as it is a lock-free, abstract way to guarantee isolated access to shared resources. But adapting for STM a program that uses lock is not simple. Besides being an error-prone task, technical details of the language might require special attention to preserve the program’s behavior. In this dissertation, we propose a set of program transformations for concurrency constructs in Haskell, a purely functional programming language. They may be used to refactor a program’s existing locks into transactional constructs from Haskell’s STM implementation. This allows a programmer to gain the benefits of working on STM even for programs which were already developed using locks. Each transformation is accompanied by execution examples and a discussion on its ability to preserve program behavior. We also present a supporting study, in which a controlled experiment was used to evaluate the benefits of locks or STM for the development of Haskell programs. Although subjects’ opinions tended to favor lock-based concurrency, those which used STM overall committed significantly fewer mistakes and required on average 12% less time to finish their assignments.
Recentemente, a queda na taxa de crescimento da quantidade de transístores integráveis em processadores tem desacelerado o crescimento de poder computacional. A lei de Moore parece aproximar-se de seu fim. Com isso, é desafiada a premissa de que software escrito hoje terá melhor desempenho no futuro simplesmente devido à evolução dos processadores. Ainda assim, aplicações paralelas ainda podem se tornar mais eficientes ao se distribuir trabalho entre diferentes processadores para execução simultânea. Para permitir a paralelização, são necessários múltiplos núcleos de processamento, o que tem levado à popularização de arquiteturas multinúcleo. Entretanto, a escrita de aplicações paralelas não é trivial. Deve-se escrever um programa para execução paralela desde sua concepção, ou adaptá-lo posteriormente para execução paralela. O programador tem a difícil tarefa de paralelização da aplicação através do uso de construções de concorrência e paralelismo. Travas, a mais comum opção para concorrência, apresentam riscos para programadores inexperientes, tais quais os famosos problemas de Deadlock e Livelock. Ao adaptarem-se de arquiteturas de um único núcleo para as de multinúcleo, as linguagens de programação precisam facilitar o uso de concorrência para os programadores. Muitos pesquisadores têm indicado Memória Transacional em Software (STM, do inglês Software Transactional Memory) como a resposta para esse problema, por ser uma forma abstrata e não bloqueante para garantia de acesso isolado a recursos compartilhados. Mas adaptar para STM programas que usam travas não é simples. Além de ser uma atividade propensa a erros, detalhes técnicos da linguagem podem requerer cuidados para se preservar o comportamento do programa. Nesta dissertação, é proposto um conjunto de transformações de programas para construções de concorrência em Haskell, uma linguagem de programação puramente funcional. Elas podem ser usadas para refatorar travas de um programa para uso de construções transacionais da implementação de STM em Haskell. Isso permite ao programador aproveitar os benefícios do trabalho com STM mesmo para programas já desenvolvidos com uso de travas. Cada transformação é acompanhada de exemplos de execução e uma discussão sobre sua capacidade de preservar o comportamento do programa. Também é apresentado um estudo de apoio, no qual um experimento controlado foi usado para avaliar os benefícios do uso de travas ou STM no desenvolvimento de programas em Haskell. Apesar das opiniões dos participantes terem favorecido o uso de travas, aqueles que usaram STM cometeram em geral menos erros e em média precisaram de 12% a menos de tempo para terminar suas tarefas.

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Dong, Yi. "Single site surface reactions : STM Studies." Doctoral thesis, Université Laval, 2018. http://hdl.handle.net/20.500.11794/30204.

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La demande des composants chimiques énantiopurs dans le secteur pharmaceutique est une des forces qui motive la recherche dans la création des catalyseurs homochiraux à la surface. La catalyse hétérogène est une méthode prometteuse pour la fabrication des produits énantiopurs puisqu'elle porte des avantages tels que la facilité de la séparation des produits désirés, la réutilisation du catalyseur et l'adaptabilité dans différentes conditions de la production en continu. La réaction d'Orito est un des exemples de la réaction hétérogène énantiosélective la plus réussie. Elle concerne l'hydrogénation de α-cétoesters sur des particules de platine modifiées par le cinchona. Il est généralement accepté que des modificateurs cinchona tels que la cinchonidine ou la cinchonine transfère la chiralité en formant des complexes bimoléculaires (complexes 1 :1) avec des réactifs prochiraux sur la surface. La compréhension de la catalyse asymétrique hétérogène au niveau fondamental est insu sante. Par contre, c'est aussi une zone fertile pour la découverte. Du progrès dans le domaine peut être réalisé par des travaux complémentaires en catalyse, en sciences des surfaces et en calcul théorique. Cette thèse décrit les études en science des surfaces inspirées par des rapports dans la littérature sur la réaction d'Orito. En plus des alcaloïdes du cinchona, qui sont des produits naturels, certains nombres de molécules synthétiques sont également des modificateurs chiraux pour la réaction d'Orito. En particulier, Baiker et ses collègues ont enquêté sur la performance du 1-(1-naphtyl)éthylamine (NEA) optiquement pur en tant que modificateur chiral pour l'hydrogénation énantiosélective de cétopantolactone (KPL) en pantolactone sur le Pt/Al2O3.1 Une partie du travail décrit dans cette thèse est l'étude des complexes formés par l'interaction de (R)-NEA et KPL sur la surface de monocristal Pt(111). Le microscope à e et tunnel (STM) est utilisé pour acquérir un grand nombre d'images des complexes KPL/(R)-NEA. Les mesures sont effectuées sur un large rapport de couverture de KPL à (R)-NEA sur la surface. Un algorithme est développé pour accélérer le comptage et la catégorisation de la forme du grand ensemble d'images STM des complexes. L'abondance de plusieurs complexes distincts qui impliquent toute une liaison hydrogène NH···O est déterminée. La prochiralité de KPL dans ces complexes sont attribuées en référant des images STM simulées par théorie de la fonctionnelle de la densité (DFT). Le rapport prochiral global (pr) mesuré dans l'expérience de la surface est comparé au rapport énantiomérique (er) mesuré par Baiker et ses collègues. Un autre algorithme est développé pour l'analyse des événements dynamiques des complexes diastéréomères individuels. Il est appliqué pour tester l'interconversion d'un état à l'autre état pendant la durée de vie de chaque complexe qui est observée par STM. Les résultats sont présentés pour les complexes formés entre 2,2,2-trifluoroacetophenone (TFAP) et (R)-NEA sur le Pt(111). Les complexes TFAP/(R)-NEA montrent des événements dynamiques qui sont décrits comme décomplexation, inversion prochirale sur site et migration intracomplexe. Les résultats sont discutés en référant les barrières énergétiques prédites par DFT pour l'hydrogénation et pour l'inversion prochirale sur site. Un rapport préliminaire présente les données quantitatives sur les interconversions des états aux états des complexes individuels des trois systèmes : TFAP/(R)-NEA, KPL/(R)-NEA et TFAP/8-Me-(R)-NEA. Le dernier modificateur de la surface concerne la substitution d'un méthyle à l'hydrogène à la position 8 du groupe naphtyle du (R)-NEA. Les observations sur les complexes KPL/(R)-NEA et TFAP/(R)-NEA sont résumés dans le contexte des données de science de surface précédemment publiées de notre groupe. La revue met l'accent sur le rôle des interactions secondaires, CH···O et CF···H, dans le contrôle stéréoscopique des molécules prochirales.
The demand for enantiopure compounds in the pharmacological sectorsisastrong driving force for research aimed at creating homochiral catalyst surfaces. Heterogeneous catalysts offer potential advantages over homogeneous catalysts including ease of separation of products from the catalyst and greater suitability for operations under continuous ow conditions. One of the most successful examples of a heterogeneous enantioselective reaction is known as the Orito reaction, the hydrogenation of α-ketoesters on cinchona modi ed platinum particles. It is believed that the cinchona modi ers operate chirality transfer by forming bimolecular surface complexes with prochiral reactants. At a fundamental level, heterogeneous asymmetric catalysis is a poorly understood area of surface chemistry. Hence, it is also a fertile area for discovery. Progress in the area can best be made by complementary work in catalysis, surface science and computation. This thesis describes surface science studies that were inspired by reports in the catalysis literature on the Orito reaction. In addition to cinchona alkaloids, which are natural products, a number of synthetic molecules have been shown to be effective chiral modifiers for the Orito reaction. In particular, Baiker and co-workers explored the performance of optically pure 1-(1-naphtyl)-ethylamine (NEA) as a chiral modifier for the enantioselective hydrogenation of ketopantolactone (KPL) to pantolactone on Pt/Al2O3.1 A major part of the work described in this thesis deals with the investigation of surface complexes formed through the interaction of (R)-NEA and KPL on single crystal Pt(111). Scanning tunnelling microscopy (STM) measurements were used to acquire a large number of images of KPL/(R)-NEA complexes. The measurements were performed over a wide ratio KPL to (R)-NEA surface coverage ratios. An algorithm was developed to enable accelerated counting and cataloguing of the large set of STM images of complexes. Therelativeabundancesofmultipledistinctcomplexationstates, allinvolvingNH·· ·O hydrogen bonding, were determined. The prochirality of KPL in these states was assigned by reference to density functional theory (DFT) simulated STM images. The overall prochiral ratio (pr) measured in the surface science experiment was compared to the enantiomeric ratio (er) measured by Baiker and co-workers. An algorithm was developed to investigate uxional events in individual diastereomeric complexes. It was applied to examine state-to-state interconversion occurring during the life times of complexes, as observed using time-lapsed STM measurements. Results are presented for complexes formed by 2,2,2-trifluoroacetophenone (TFAP) interacting with (R)-NEA on Pt(111). The TFAP/(R)-NEA complexes show dynamic events that we describe as decomplexation, on-site prochiral inversion and intracomplex migration. The results are discussed in relation to energy barriers predicted by DFT for hydrogenation and for on-site prochiral inversion. Quantitative data for state-to-state interconversion in single complexes are presented for three systems: TFAP/(R)-NEA, KPL/(R)-NEA and for TFAP interacting with methyl-substituted (R)-NEA. A preliminary analysis of the data is presented. The observations on KPL/(R)-NEA and TFAP/(R)-NEA complexes are reviewed within the context of previously published surface science data from our group. The review emphasizes the role of secondary interactions, CH···O and CF···H bonding, in the stereocontrol of prochiral molecules.

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Vianna, Camila Pereira. "Papel da proteína STI1 na via de sinalização Rnd1 - p190RhoGAP." reponame:Repositório Institucional da UFPR, 2017. http://hdl.handle.net/1884/53519.

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Orientador : Prof. Dr. Silvio Marques Zanata
Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Ciencias Biológicas (Microbiologia, Parasitologia e Patologia Básica). Defesa: Curitiba, 2017
Inclui referências : f. 55-60
Resumo: A proteína STI1 foi descrita como uma molécula relacionada ao estresse térmico de leveduras, e por isso é denominada Stress-Inducible Protein 1. Sua homóloga humana é a Hop (Heat-shock organizing protein). Ela tem expressão praticamente ubíqua e é encontrada em vesículas intracelulares, complexo de Golgi ou dispersa no citoplasma. Estudos indicam que esta proteína participa de vários eventos celulares como desenvolvimento de astrócitos, diferenciação de neurônios, neuroproteção, neuritogênese, formação da memória em ratos e proliferação celular em tumor de ovário. Além disso, a STI1 foi também recentemente caracterizada como ligante da GTPase Rnd1. As GTPases de baixa massa molecular são um grupo de moléculas que ciclam entre as formas ativa e inativa. Aquelas pertencentes à subfamília Rnd possuem pouca atividade GTPásica intrínseca, encontrando-se constitutivamente ativas, sendo desse modo diferentes das outras Rho GTPases. A proteína Rnd1 é encontrada principalmente no cérebro, e está envolvida em vários mecanismos celulares, como a inibição de fibras de estresse e a indução da desorganização do citoesqueleto de actina e adesão focal. Além disso, Rnd1 está presente na extensão inicial de neuritos em células PC-12, e no desenvolvimento de dendritos em neurônios hipocampais de ratos. Foi demonstrada que a interação da STI1 com a Rnd1 pode interferir na fenomenologia (colapso do cone de crescimento) desencadeada pelo eixo Sema3A/Plexina-A1. Por outro lado ainda não foi determinado quais são as vias de sinalização que estão a jusante da interação STI1- Rnd1, responsáveis por esta interferência. Desse modo, as proteínas recombinantes GST, GST-RhoA G14V e GST-RBD foram expressas para a realização de ensaios de pulldown visando elucidar o papel de STI1 na atividade de p190RhoGAP e seu substrato RhoA. Primeiramente foi possível detectar que a presença de STI1 ao inativar Rnd1, leva também a inativação de sua ligante p190RhoGAP. Porém, não foi possível esclarecer o papel desta proteína na atividade de RhoA bem como sua atuação na atividade de cofilina. A produção de anticorpo monoclonal anti-Rnd1 também foi um objetivo do presente trabalho, porém apesar da indicação da presença de anticorpos anti-Rnd1 em soro policlonal, não foi possível detectar a clone positivo para este anticorpo na produção de hibridomas. Palavras-chave: GTPases, Rnd1, STI1, atividade.
Abstract: STI1 protein has been described as a yeast thermal stress-related molecule, and is therefore called Stress-Inducible Protein 1. Its human counterpart is Hop (Heat-shock organizing protein). It has virtually ubiquitous expression and is found in intracellular vesicles, Golgi complex or dispersed in the cytoplasm. Studies indicate that this protein participates in several cellular events such as astrocyte development, differentiation of neurons, neuroprotection, neuritogenesis, memory formation in rats and cell proliferation in ovarian tumor. In addition, STI1 has also recently been characterized as GTPase Rnd1 linker. Low molecular weight GTPases are a group of molecules that cycle between active and inactive forms. Those belonging to the subfamily Rnd have little intrinsic GTPase activity, being constitutively active, thus being different from the other Rho GTPases. Rnd1 protein is found primarily in the brain, and it is involved in several cellular mechanisms, such as inhibition of stress fibers and induction of actin cytoskeleton disorganization and focal adhesion. In addition, Rnd1 is present in the initial extension of neurites in PC-12 cells, and in the development of dendrites in hippocampal neurons of rats. It has been shown that the interaction of STI1 with Rnd1 can interfere in the phenomenology (growth cone collapse) triggered by the Sema3A / Plexin-A1 axis. On the other hand, it has not yet been determined which are the signaling pathways that are downstream of the STI1-Rnd1 interaction, responsible for this interference. Thus, the recombinant GST, GST-RhoA G14V and GST-RBD proteins were expressed for pulldown assays to elucidate the role of STI1 in p190RhoGAP activity and its RhoA substrate. First, it was possible to detect that the presence of STI1 when inactivating Rnd1 also leads to the inactivation of its p190RhoGAP ligand. However, it was not possible to clarify the role of this protein in RhoA activity as well in cofilin activity. The production of anti-Rnd1 monoclonal antibody was also an objective of the present work, but despite the presence of anti-Rnd1 antibodies in polyclonal serum, it was not possible to detect the positive clone for this antibody in the production of hybridomas. Key words: GTPases, Rnd1, STI1, activity.

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22

Shao, Jianfei. "STM/STS and BEES Study of Nanocrystals." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/10526.

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This work investigates the electronic properties of very small gold and semiconductor particles using Scanning Tunneling Microscopy/Spectroscopy (STM/STS) and Ballistic Electron Emission Spectroscopy (BEES). Complementary theoretical works were also performed. The first theoretical work was to calculate the quantized states in the CdS/HgS/CdS quantum-well-quantum-dot nanocrystals. An eight-band envelope function method was applied to this system. This method treats exactly the coupling between the conduction bands, the light-hole bands, the heavy-hole bands, and the spin-orbit split bands. The contributions of all other bands were taken into account using second order perturbation theory. Gold nanocrystals with diameters of 1.5 nm have discrete energy levels with energy spacings of about 0.2 eV. These values are comparable to the single electron charging energy, which was about 0.5 eV in our experimental configuration. Since bulk gold doesnt have an energy gap, we expect the electron levels both below and above the Fermi level should be involved in the tunneling. Measured spectroscopy data have rich features. In order to understand and relate these features to the electronic properties of the nanocrystals, we developed a tunneling model. This model includes the effect of excited states that have electron-hole pairs. The relaxation between discrete electron energy levels can also be included in this model. We also considered how the nanocrystals affect the BEES current. In this work an ultra-high vacuum and low-temperature STM was re-designed and rebuilt. The BEEM/BEES capabilities were incorporated into the STM. We used this STM to image gold nanocrystals and semiconductor nanocrystals. STS and BEES spectra of gold nanocrystals were collected and compared with calculations.

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Liu, Jun. "Neo--- A new perspective on STM capacity." Thesis, Georgia Institute of Technology, 2004. http://hdl.handle.net/1853/5034.

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Exploring the word length effect from the perspective of information density, the current research extended previous findings on cross-linguistic differences in STM capacity with the development of a new strategy that has the potential to double ones digit span with minimal learning and a much shorter training period. Experiments have shown promising results and responses to training differed across language groups. The underlying mechanisms are explored and discussed in relation to strategy usage, capacity estimates and optimization of language systems.

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Martins, Bruno Vieira da Cunha. "Desenho e construção de um UHV-STM." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/277568.

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Orientador: Daniel Mario Ugarte
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin
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Resumo: O estudo da estrutura de nanosistemas individuais requer o uso de equipamentos capazes de gerar imagens de sistemas com poucos átomos. No caso de nanopartículas metálicas produzidas por síntese química, uma questão relevante e ainda pouco estudada é a organização dos passivantes sobre sua superfície e como isso contribui para a definição de sua estrutura de equilíbrio. Para abordar este tema, devemos ser capazes de gerar imagens de resolução atômica em superfícies com alto grau de curvatura: a microscopia de tunelamento (STM) representa o instrumento mais adequado para este tipo de tarefa. Entretanto, o estudo detalhado requer o uso de métodos não-convencionais de microscopia STM (ex. modulação da tensão de bias ou de setpoint), sendo assim desejável que tenhamos total controle sobre a operação do instrumento. Este domínio preciso sobre as características funcionais consiste na principal razão que justifica a construção de um STM no próprio grupo. Este trabalho descreve o desenho, a construção e a caracterização de um STM de Ultra-Alto Vácuo (UHV). Todo o desenho e a construção foram integralmente realizadas no grupo de pesquisa. Apresentamos e justificamos os parâmetros escolhidos para o projeto, os quais definem o perfil do instrumento. O projeto mecânico consiste em um sistema elástico tipo ¿Parallel-Guiding-Spring Table¿(PSM). O sistema de varredura foi desenvolvido utilizando na configuração tipo tripod para os atuadores piezoelétricos. Desenvolvemos dois protótipos da cabeça STM, ambos compatíveis com UHV. Apresentamos o projeto e a construção da câmara de vácuo e do sistema de amortecimento de vibração. Na parte eletrônica, desenvolvemos um projeto que envolve blocos anal'ogicos de precisão e componentes digitais de 16 bits. O sistema funciona com baixa tensão, o que o torna mais estável e menos suscetível ao ruído e a variações térmicas. O sistema de controle embarcado e seu modelo analítico são analisados de modo a se determinar os parâmetros para operação estável. Caracterizamos todo o sistema e obtivemos imagens para superfícies de Grafite e Au como forma de verificar a performance do equipamento construído. Por fim discutimos as dificuldades do projeto e apresentamos soluções para os pontos que requerem certa otimização
Abstract: The study of the structure of individual nanosystems requires the use of equipments capable of generating images of systems containing just a few atoms. In the case of metallic nanoparticles produced by chemical synthesis, a relevant and not much studied question is the organization of the passivant molecules over the surface and how they contribute to the definition of the equilibrium structure. To adress this issue, we must be capable of generating atomic resolution images on surfaces with a high level of curvature: the Scanning Tunneling Microscopy (STM) represents the most adequate instrument for this job. Nevertheless, the detailed study requires the use of non-conventional methods of STM microscopy (ex. bias voltage and setpoint modulation), then it is desirable to have total control over the instrument operation. This precise domain over the functional characteristics consists in the main reason that motivated the construction of a STM in our group. This work describes the design, construction and characterization of an Ultra-High Vacuum (UHV) STM. The design and construction were both integrally done in our research group. We present and justify the chosed project parameters, which define the profile of the instrument. The mechanical project consists of an elastic system of the ¿Parallel-Guiding- Spring-Table Mechanism¿(PSM) type. The scanning system was developed using the tripod configuration for the piezoelectric actuators. We have developed two prototypes for the STM head, both compatible with UHV. We present the project and construction of the vacuum chamber and the vibration isolating system. For the electronics, we have developed a project that involves precision analog blocks and 16 bits digital components. The system works with low voltage, what turns it more stable e less succeptible to noise and thermal variations. The embedded control system and its model are analysed in order to determine the stable operation parameters. We have characterized the system in detail and obtained images for Graphite and Gold surfaces as a way to verify the performance of the constructed equipment. Finally, we discuss the difficulties of the project and present solutions for the points that require optimization
Doutorado
Física da Matéria Condensada
Doutor em Ciências

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Leandro, Silvana Castro [UNESP]. "Batimentos quânticos dependentes do SPIN via STM." Universidade Estadual Paulista (UNESP), 2013. http://hdl.handle.net/11449/91985.

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Neste trabalho investigou-se teoricamente a densidade local de estados (LDOS) sondada por uma ponta de STM de metais hospedando um átomo adsorvido e uma impureza subsuperficial. Modelamos o sistema por meio do Hamiltoniano de Anderson de duas impurezas. Utilizando-se do procedimento da equação de movimento nas funções de Green, derivamos expressões analíticas para a LDOS de dois tipos de hospedeiro: uma superfície metálica e um fio quântico. A LDOS revela oscilações de Friedel e interferência Fano como função da posição da ponta. Essas oscilações dependem fortemente da dimensão do hospedeiro. Encontramos que os números de onda de Fermi dependentes do spin dão origem a batimentos quânticos spin-polarizados na LDOS. Embora a LDOS da superfície mostre um padrão de batimentos amortecidos, ela possui um comportamento oposto no fio quântico. Devido a ausência de amortecimento, o fio opera como um filtro de spins espacialmente resolvido com elevada eficiência.
We theoretically investigate the local density of states (LDOS) probed by an STM tip of ferromagnetic metals hosting a single adatom and a subsurface impurity. We model the system via the two-impurity Anderson Hamiltonian. By using the equation of motion with the relevant Green’s functions, we derive analytical expressions for the LDOS of two host types: a surface and a quantum wire. The LDOS reveals Friedel-like oscillations and Fano interference as a function of the STM tip position. These oscillations strongly depend on the host dimension. Interestingly, we find that the spin-dependent Fermi wave numbers of the hosts give rise to spin-polarized quantum beats in the LDOS. Although the LDOS for the metallic surface shows a damped beating pattern, it exhibits the opposite behavior in the quantum wire. Due to this absence of damping, the wire operates as a spatially resolved spin filter with a high efficiency.

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Leandro, Silvana Castro. "Batimentos quânticos dependentes do SPIN via STM /." Ilha Solteira, 2013. http://hdl.handle.net/11449/91985.

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Orientador: Antonio Carlos Ferreira Seridonio
Banca: Devaney Ribeiro do Carmo
Banca: Guillermo Gerardo Cabrera Oyarzun
Resumo: Neste trabalho investigou-se teoricamente a densidade local de estados (LDOS) sondada por uma ponta de STM de metais hospedando um átomo adsorvido e uma impureza subsuperficial. Modelamos o sistema por meio do Hamiltoniano de Anderson de duas impurezas. Utilizando-se do procedimento da equação de movimento nas funções de Green, derivamos expressões analíticas para a LDOS de dois tipos de hospedeiro: uma superfície metálica e um fio quântico. A LDOS revela oscilações de Friedel e interferência Fano como função da posição da ponta. Essas oscilações dependem fortemente da dimensão do hospedeiro. Encontramos que os números de onda de Fermi dependentes do spin dão origem a batimentos quânticos spin-polarizados na LDOS. Embora a LDOS da superfície mostre um padrão de batimentos amortecidos, ela possui um comportamento oposto no fio quântico. Devido a ausência de amortecimento, o fio opera como um filtro de spins espacialmente resolvido com elevada eficiência.
Abstract: We theoretically investigate the local density of states (LDOS) probed by an STM tip of ferromagnetic metals hosting a single adatom and a subsurface impurity. We model the system via the two-impurity Anderson Hamiltonian. By using the equation of motion with the relevant Green's functions, we derive analytical expressions for the LDOS of two host types: a surface and a quantum wire. The LDOS reveals Friedel-like oscillations and Fano interference as a function of the STM tip position. These oscillations strongly depend on the host dimension. Interestingly, we find that the spin-dependent Fermi wave numbers of the hosts give rise to spin-polarized quantum beats in the LDOS. Although the LDOS for the metallic surface shows a damped beating pattern, it exhibits the opposite behavior in the quantum wire. Due to this absence of damping, the wire operates as a spatially resolved spin filter with a high efficiency.
Mestre

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27

Robertson, Derek. "Variable processing of flavours in rat STM." Thesis, University of St Andrews, 1985. http://hdl.handle.net/10023/14682.

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The research reported in this thesis examines factors that affect the willingness of rats to ingest novel flavour solutions. Emphasis is placed on the memorial processes assumed to underlie the decision as to whether or not a solution is "safe" to drink. Rats exhibit caution (neophobia) in consuming an unfamiliar (target) solution. This unconditional response to novelty habituates as the rat acquires experience with the target solution (provided that ingestion of the target solution has no noxious consequences!). Neophobia to the target solution may be restored, however, if another (distractor) solution is presented during the interval separating pre-exposure to, and testing of, the target solution (Green & Parker, 1975). In Section 1, the phenomena of habituation to an iterated target stimulus and the disruption of this process by a distractor are introduced. Theoretical explanations of the "dishabituation" effect of a distractor stimulus are described and assessed. The possibility of an empirical test of the relative validity of the Robertson and the Wagner hypotheses using the attenuation of flavour neophobia procedure of Green and Parker provided the impetus for the experiments reported in Section 2. In Section 3, attention is drawn to the similarity of the procedure designed to establish habituation and that Intended to establish latent inhibition to a stimulus. A limited review of empirical data is presented testifying to the fact that habituation and latent inhibition are affected similarly by identical parameter manipulations. The Wagner (1976) model views habituation and latent inhibition as the outcome of a common underlying process, Expts. 10a and 10b, therefore, sought to determine whether latent inhibition of a conditioned taste aversion (CTA) to lemon or sucrose solution would be affected by a coffee distractor in a manner consonant with predictions derived from the results of the neophobia experiments reported in Section 2. The distractor, however, had no effect on strength of latent inhibition in either experiment. Expt. 11c demonstrated that it is possible for a distractor (30% vanilla) to disrupt attenuation of neophobia to a target flavour (3% cider vinegar) without affecting latent inhibition to the target flavour, i.e., there is no direct correspondence between measures of habituation and latent inhibition to the same stimulus. In Section 4, the phenomena of overshadowing and potentiation of a CTA are introduced. At least one explanation of potentiation (c.f., Durlach & Rescorla, 1980) stresses the importance of an association between the elements of a compound CS. Rescorla and Furrow (1977) found interstimulus associations were formed more rapidly between similar rather than dissimilar stimuli. Given these results, Expts. 12a and 12b sought to determine whether a single sequential presentation of lemon and coffee (similar solutions) paired with LiCl would result in potentiation of a conditioned aversion to the lemon solution and whether a single sequential presentation of sucrose and coffee (dissimilar solutions) paired with LiCl would result in overshadowing of a conditioned aversion to the sucrose solution. These experimental predictions were confirmed. In Section 5, a potential confound in the neophobia experiments is addressed. Interpretation of attenuated neophobia as a habituation process is defended and alternatives to the Wagner (1976) theory of habituation are considered for their ability to encompass the data reported in Section 2. Only the Wagner model, however, appears able to account for all the data. Nevertheless, some limitations of the model are indicated. Finally, the conditions promoting overshadowing and potentiation of a CTA are discussed.

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Pavelec, Jiří. "Vývoj lineárního posuvu pro UHV STM/AFM." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2011. http://www.nusl.cz/ntk/nusl-229812.

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The aim of this diploma thesis is to develop a linear positioning stage for Ultra High Vacuum (UHV) environment. Simple prototypes of the linear positioning stage were designed and incorporated as part of a multiaxis sample manipulator for a UHV Scanning Tunneling Microscopy / Atomic Force Microscopy (STM/AFM). Different types of position encoders and linear guideways are discussed. Implementation of the homodyne interferometer as an optimization tool for a slip-stick based linear stage is described. Scalar diffraction theory is used to model the diffraction grating optical position encoder behavior.

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Lur, Gyorgy. "STIM1, Orai1 and store operated calcium entry in pancreatic acinar cells." Thesis, University of Liverpool, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.539501.

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Saliba, Youakim. "Identification des partenaires de STIM1 dans le cœur normal et hypertrophié." Paris 6, 2012. http://www.theses.fr/2012PA066541.

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Nous avons déjà démontré un rôle important de STIM1 dans l’induction de l’hypertrophie cardiaque, mais l’identité des canaux STIM1 dépendants responsables de ce flux calcique pro-hypertrophique dans les cellules ventriculaires du rat reste à déterminer. Dans cette étude, nous avons développé une nouvelle méthode de transfert myocardique de gène non viral, en utilisant l’énergie des ultrasons, des liposomes et des injections pressurisées dans le myocarde du rat. Grâce à sa simplicité, son efficacité et sa faible immunogénicité, cette technique a produit un nombre suffisant de cellules transfectées pour effectuer des expériences biochimiques et physiologiques sur cellules isolées. Nous avons ensuite caractérisé le profil d’expression des protéines ORAIs et TRPCs dans les cellules ventriculaires normales et hypertrophiées, et avons trouvé une augmentation de l’expression de TRPC1 dans l’hypertrophie cardiaque. Ensuite nous avons utilisé la méthode de transfert de gènes pour identifier les partenaires canalaires de STIM1 via l’ARN interférence par injection de siARN. Nous avons identifié TRPC5 comme un canal calcique non-sélectif qui fonctionne d’une façon constitutive en conditions basales, avec une activité accrue dans l’hypertrophie cardiaque ; ainsi que ORAI3 qui opère dans deux modes: entrée capacitative de calcium et entrée constitutive en concordance avec TRPC5. Nous avons développé une nouvelle méthode de transfert myocardique de gène non viral que nous avons ensuite utilisée pour identifier TRPC5 et ORAI3 comme nouveaux canaux voltage indépendants et STIM1 dépendants dans les myocytes ventriculaires de rat
We previously showed an important role of STIM1 in cardiac hypertrophy; however, the identity of the channels responsible for the STIM1 dependent pro-hypertrophic Ca2+ entry in the rat ventricular myocytes remains to be elucidated. In this study we developed a new method of myocardial non viral gene delivery, by using the combination of ultrasound energy (USE), liposomes and high pressure injections to the rat heart. Due to its simplicity, low toxicity and low immunogenicity, this method produced sufficient number of transfected cells to perform biochemical experiments and single cell physiological measurements. We then characterized the expression profile of TRPCs and ORAIs proteins in both normal and hypertrophied ventricular myocytes, and found an upregulation of TRPC1 in hypertrophied cells. We further used the new gene delivery method to identify and screen for the STIM1 associated channel candidates via RNA interference. We identified TRPC5 as a non-selective Ca2+ channel that operates constitutively in basal conditions with increased activity in cardiac hypertrophy, as well as ORAI3 that functions in both modes: SOCE and constitutive basal Ca2+ entry in concordance with TRPC5. We developed an efficient non-viral cardiac gene delivery which we used to elucidate TRPC5 and ORAI3 as new voltage independent STIM1 regulated Ca2+ channels in the ventricular rat myocytes

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Gueder, Nahla. "sp²-Iminosugar-glucosidases inhibitor 1-C-octyl-2-oxa-3-oxocastanospermine - induced antiproliferative, apoptotic and necrotic effects in breast cancer cells via targeting GRP78, Stim1 and Orai1." Thesis, Amiens, 2018. http://www.theses.fr/2018AMIE0033/document.

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L'altération de glycosylation est l'une des caractéristiques du cancer du sein. Ainsi le défaut de glycosylation affecte différentes protéines glycosylées responsables des différents processus cancéreux. Les canaux SOC (Store operated channels) constituent la voie majeure de l'entrée du calcium dans les cellules et sont impliqués dans la prolifération, la migration et la survie des cellules cancéreuses du sein. CO-OCS est un nouvel inhibiteur de la glycosylation avec plus de sélectivité vis-à-vis des α-glucosidases, et montre des activités anticancéreuses des cellules cancéreuses du sein, sans affecter les cellules mammaires normales. L'objectif de ma thèse est d'étudier les mécanismes moléculaires par lesquels CO-OCS induit ses effets anti-tumoraux. CO-OCS inhibe la migration des cellules cancéreuses à fort potentiel métastatique. Cet effet anti-migratoire est dû à une réduction de l'expression de la β1-intégrine, de Stim1, et de l'activation des voies de signalisation FAK et ERK1/2 par CO-OCS. Dans les cellules cancéreuses peu invasives, CO-OCS diminue la prolifération et augmente la mortalité de ces cellules en affectant l'expression de 3 protéines : Stim1 et Orai1 : protéines N-glycosylées au niveau du réticulum endoplasmique (RE), et GRP78, protéine de stress du RE. Ainsi en supprimant complétement l'expression de Stim1, CO-OCS réduit la prolifération en accumulant les cellules dans les phases G1 et G2/M du cycle cellulaire. Alors que la réduction de l'expression de GRP78 et d'Orai1 par le CO-OCS augmente respectivement l'apoptose et la nécrose. Par ailleurs, l'invalidation de Stim1 atténue l'effet apoptotique induit par CO-OCS. CO-OCS réduit aussi le contenu calcique du RE. Cette réduction du calcium réticulaire est due à une fuite de calcium par le Translocon. En effet, l'Anisomycine, inhibiteur du Translocon, restore de contenu calcique réticulaire et antagonise l'apoptose induite par le CO-OCS. En conclusion, CO-OCS induit une accumulation de protéines mal-repliées dans le RE induisant ainsi un stress réticulaire. Trois cibles du CO-OCS ont été identifiées : l'expression de Stim1 favorise la prolifération tandis que celle d'Orai1 et de GRP78 protègent respectivement les cellules de l'apoptose et de la nécrose induites par CO-OCS. De plus, en diminuant l'expression de GRP78, CO-OCS induit une fuite du calcium du RE par le Translocon
Alteration in glycosylation pattern is one of the hallmarks of breast cancer. The levels and the abnormal expressions of glycan were found in breast cancer patients. Glycosylation defect can affect different glycosylated proteins which are implicated in cancerogenesis. Changes in intracellular Ca2+ levels can regulate different cellular processes. SOC channels are implicated in breast cancer proliferation, migration and survival. CO-OCS is a new glycosylation inhibitor with more selectivity toward theα- glucosidases exhibited anti-cancer activities in breast cancer cells without affecting the normal mammary cells. The objective of my thesis is investigating the related molecular mechanisms by which CO-OCS induced its anti-tumour effects.CO-OCS impaired breast cancer migration through decrease β1-integrin expression and the activation of FAK and ERK1/2 signalling pathways. CO-OCS also induced anti-migratory effect via Stim1 protein expression down-regulation leading to inhibition of SOCE. Additionally, CO-OCS affected the expression of both Orai1 and Stim1 proteins leading to anti-proliferative effects and cell cycle arrest in G1 and G2/M phase respectively. Moreover, CO-OCS affected the expression of Stim1 at the protein level without affecting its transcript level. GRP78 implicated in CO-OCS apoptotic death. The expression of Stim1 regulated the apoptosis induced by CO-OCS via modulating GRP78 expression. Orai1 down-regulation promoted CO-OCS necrotic effect. CO-OCS induced ER- calcium depletion due to increase in ER calcium leak via the Translocon; Anisomycin (Translocon inhibitor) decreased the apoptosis induced by CO-OCS. In conclusion, these results show that in breast cancer, by targeting Stim1, Orai1 and GRP78, CO-OCS reduced cell proliferation and induced apoptosis and necrosis cell death. Stim1 favours CO-OCS apoptotic effect while Orai1 protected from necrosis induced by CO-OCS. The inhibition of Translocon decreased CO-OCS apoptotic cell death via restoring the ER calcium homeostasis

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Le, Sueur Hélène. "Un AFM-STM cryogénique pour la physique mésoscopique." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2007. http://tel.archives-ouvertes.fr/tel-00261434.

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La spectroscopie électronique basée sur l'effet tunnel donne accès à la densité d'états des électrons (DoS) dans les matériaux conducteurs, et renseigne ainsi en détail sur leurs propriétés électroniques.
Au cours de cette thèse, nous avons développé un microscope permettant d'effectuer la spectroscopie tunnel résolue spatialement (10 nm) de nanocircuits individuels, avec une résolution en énergie inégalée (10 µeV). Cet appareil combine les fonctions de Microscopie par Force Atomique (mode AFM) et de spectroscopie Tunnel locale (mode STM), et fonctionne à 30 mK. Dans le mode AFM, la topographie de l'échantillon est imagée grâce à un diapason en quartz piézoélectrique, ce qui permet de repérer les circuits. La spectroscopie tunnel peut ensuite être faite sur les zones conductrices.
Avec ce microscope, nous avons mesuré la DoS locale dans une structure hybride Supraconducteur-métal Normal-Supraconducteur (S-N-S). Dans un tel circuit, les propriétés électroniques de N et de S sont modifiées par l'effet de proximité supraconducteur. Notamment, pour des fils N courts, nous avons pu observer -comme prédit- la présence d'un gap dans sa DoS, indépendant de la position dans la structure : le “minigap”. De plus, en modulant la phase supraconductrice entre les deux S, nous avons mesuré la modification de ce gap, et sa disparition lorsque la différence de phase vaut π.
Nos résultats expérimentaux pour la DoS, ainsi que ses dépendances en phase, en position, et en longueur de N sont en accord quantitatif avec les prédictions de la théorie quasiclassique de la supraconductivité. Certaines de ces prédictions sont observées pour la première fois.

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Pham, Van Dong. "STM characterization of functionalized carbon nanotubes and graphene." Sorbonne Paris Cité, 2015. http://www.theses.fr/2015USPCC245.

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Dans cette thèse, nous avons étudié l'interaction entre des molécules organiques et des nanomatériaux de carbone. En utilisant un microscope à effet tunnel (STM) à basse température et sous ultra-vide, nous avons mesuré les propriétés de molécules de porphyrine physisorbées sur du graphène ou des nanotubes de carbone. Nous avons d'abord étudié l'injection d'électrons dans le graphène sur des défauts (joints de grains et atomes d'azote insérés). Une étude d'états image résonants nous a également permis de mettre en évidence une variation locale du travail de sorite dans le graphène dopé. Nous avons ensuite étudié les propriétés de molécules de porphyrine (H2TPP) adsorbées sur une surface Au(111). En utilisant la pointe du microscope nous avons induit des réactions de tautomérisation et de déshydrogénation et montré comment cela modifie les états moléculaires et l'interaction molécule-surface. Nous avons ensuite étudié l'interaction du graphène avec des molécules de porphyrine. Nous avons montré que le couplage électronique est faible entre les molécules et le graphène. Nous avons ensuite montré comment un atome d'azote inséré dans le réseau de carbone du graphène modifie l'interaction molécule-surface. Une diminution de l'énergie des états moléculaires au niveau des sites dopants révèle un transfert de charge partiel entre les sites d'azote et les molécules. Dans la dernière partie, nous avons étudié les propriétés de nanotubes de carbone monoparois fonctionnalisés par un polymère de porphyrine. Les mesures ont révélé que le polymère couvre partiellement les nanotubes. La spectroscopie locale a indiqué que la densité d'états locale est modifiée au niveau du polymère
In this thesis we studied the interaction between organic molecules and carbon nanomaterials. Using scanning tunneling microscopy (STM) at low temperature and in ultra-high vacuum, we measured the properties of porphyrin molecules at the surface of graphene and single-walled carbon nanotubes. We first studied electron injection in graphene at defect sites (grain boundaries and nitrogen doping atoms). Using image-potential states, we evidenced the variation of local work function in doped graphene. Secondly, we investigated the properties of free-base porphyrin (H2TPP) molecules adsorbed on a Au(111) surface. We performed tip-induced tautomerization and dehydrogenation of the molecules, and revealed how these operations modify the molecular states and molecule-substrate interaction. Following these two preliminary studies, we studied the interaction of graphene with porphyrin molecules. We evidenced a weak electronic coupling between the molecules and graphene. We then showed how a nitrogen dopant on doped graphene can tune the molecule-surface interaction. The comparison between molecules adsorbed on nitrogen doping sites with those adsorbed on carbon sites clearly reveals a downshift of the energy of the molecular states at the doping sites. This downshift reveals a partial electron transfer from the nitrogen sites of graphene to the adsorbed molecules. In the last part of this thesis, we studied the properties of single-walled carbon nanotubes functionalized with a porphyrin polymer. The STM measurements revealed that the polymer is partially covering the nanotubes. Local spectroscopy indicated that the local density of states are modified at the polymer location

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Vinet, Maud. "Etude par stm de nanostructures supraconductrices par proximite." Université Joseph Fourier (Grenoble), 2001. http://www.theses.fr/2001GRE10047.

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Cette these a ete motivee par le desir d'etudier l'effet de proximite entre un metal normal (n) et un supraconducteur (s). Pour cela, nous avons construit un microscope a effet tunnel (stm) pour mesurer la densite d'etats electroniques locale d'un metal. Celui-ci fonctionne a 100 mk dans un cryostat a dilution renverse. Pour respecter la philosophie de ce cryostat original, le stm est thermalise par contacts mecaniques sur la boite de melange sans gaz d'echange. Avant de coupler le stm a la dilution, nous avons procede a une mise au point prealable dans un cryostat a 4he a des temperatures comprises entre 4,2 k et 1,5 k. Nous avons donc etudie l'effet de proximite entre de l'or (n) en bon contact electrique avec du niobium (s) a 1,5 k. La reflexion d'andreev est le mecanisme microscopique qui regit cet effet de proximite. Elle permet a electron incident d'energie au dessus du niveau de fermi qui arrive sur une interface avec un supraconducteur d'etre retro-reflechit en un trou d'energie -. La paire electron-trou correles ainsi creee dans le metal normal se propage de maniere coherente sur une distance l hd/. Ces correlations conduisent a un affaiblissement de la densite d'etats a une particule dans le metal normal. Lorsque l'or est de taille infinie, 1 m dans notre cas, nous observons un affaiblissement de la densite d'etats electroniques locale dont l'extension spectrale diminue lorsque l'on s'eloigne de l'interface. Physiquement, c'est une manifestation de la longueur l. Les spectres mesures sont quantitativement expliques par le formalisme quasi-classique de l'equation d'usadel. Lorsque l'or est en contact avec le niobium est de faibles dimensions, quelques dizaines de nanometres, la densite d'etats montre un minigap

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35

Voňka, Jakub. "Návrh a ověření nízkoteplotní části UHV - STM mikroskopu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2013. http://www.nusl.cz/ntk/nusl-230611.

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The diploma thesis addresses the design and experimental verification of cooling system and low temperature part of UHV - STM working in temperature range of 20K - 300K. Due to the demand of variable temperature, the flow cooling system with cryogenic (~5 K) helium (He) is used. Two variants of the low temperature part of the microscope are studied. First the version with cooling only the sample holder, and second with cooling of the whole STM. Designed cooling system consists of He flow cryostat allowing to connect it to the Dewar vessel with liquid helium (LHe) using a low-loss transfer line. The cryostat consists of He inlet and outlet, heat exchangers and copper strains (i.e. braids) for the thermal connection of the sample holder/STM and radiation shield around the STM with the heat exchangers. The thesis describes the design of the flow cryostat and its initial tests in the designed vacuum chamber. Heat flow through a spot contact is also discussed to estimate thermal conductance of insulation supports based on thermal resistance of spherical contacts. The thesis was elaborated in collaboration with the Institute of Scientific Instruments of the ASCR, v.v.i.

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Dao, Tomáš. "Návrh nosné platformy pro nízkoteplotní UHV STM mikroskop." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2014. http://www.nusl.cz/ntk/nusl-231317.

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Diploma thesis deals with the design of a vibration isolated platform for low temperature scanning tunneling microscope working under ultra high vacuum (UHV STM). Cooling of the microscope is done by liquid helium using a flow cryostat designed in Institute of Scientific Instruments of the AS CR. In the thesis, general requirements of designing of an ultra high vacuum compatible devices are discussed, as well as the ways of vibrational isolation and damping. Also some ways how to restrict the transfer of vibration between vacuum devices and surroundings are mentioned. This knowledge is then applied to the design of the antivibrational microscope platform compatible with low temperature usage. For better understanding of vibrational transfer and damping, a real model of the designed platform is made and vibrational transfer characteristics are measured and compared with the theory.

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Clark, Kendal W. "STM Study of Molecular and Biomolecular Electronic Systems." Ohio University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1282363151.

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McElroy, Cameron Shea. "The Role of SULT2 ST1 in Zebrafish Development." University of Toledo / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1273786802.

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Willis, Mary L. "STM Studies of Oxygen Etching of Silicon Surfaces." VCU Scholars Compass, 2005. http://scholarscompass.vcu.edu/etd/1008.

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This study uses atomic force microscopy (AFM) to investigate the oxygen etching behavior of the following silicon surface orientations: (001), (111), (113), (5 5 12) and (112). Most etching was performed at sample temperatures between 650 °C and 800 °C, at pressures of 3.3×10-7 and 1.5×10-7 Torr, and at an exposure of 200 L. Surface orientation strongly influences the morphology resulting from extended etching. The surface orientations that are stable against etching and remain flat include Si(001), Si(111), and Si(113). Such surfaces also include island structures, which result from etching around oxide-induced pinning sites. The density of these islands increases at lower temperatures and higher pressures. The surface orientations that are unstable against oxygen etching and facet to other orientations include Si(5 5 12) and Si(112). These surfaces form sawtooth facets that are primarily composed of more stable (111) and (113) planes. By controlling the temperature and exposure during oxygen etching, it is therefore possible to form a variety of surface morphologies.

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Premsler, Thomas [Verfasser], Albert [Akademischer Betreuer] Sickmann, and Jan Georg [Gutachter] Hengstler. "Mass spectrometry based interaction study of the STIM1 and VASP proteins : (Massenspektrometrie-basierte Interaktionsstudie der Proteine STIM1 und VASP) / Thomas Premsler. Betreuer: Albert Sickmann. Gutachter: Jan Georg Hengstler." Dortmund : Universitätsbibliothek Dortmund, 2012. http://d-nb.info/1110892373/34.

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Schmid, Andreas B. "The adaptor protein Sti1/Hop connects the Hsp70 and Hsp90 chaperone cycle /." München : Verl. Dr. Hut, 2009. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=018860584&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.

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Mateo, Montalcini Solange A. "AGC kinase Sta1 is a virulence determinant in the rice blast fungus." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531838.

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Ahmed, Jubed Omee. "Characterisation of the roles of Poz1 and Stn1 at Schizosaccharomyces pombe telomeres." Thesis, University of Sussex, 2014. http://sro.sussex.ac.uk/id/eprint/48855/.

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Telomeres protect the ends of chromosomes from the activity of DNA repair machinery and provide a solution to the end-replication problem. In humans, the core protein complex located at telomeres is known as shelterin and consists of six protein subunits. Although variation is seen in the telomeric complex between species, in fission yeast the complex has notable similarities to that of humans. Separately to shelterin, the CST complex (Cdc13/Stn1/Ten1) is conserved in budding yeast, plants and mammals and is thought to negatively regulate telomerase, in addition to being required for telomere protection. However, unlike Stn1 and Ten1, Cdc13 has not yet been identified in fission yeast. Poz1 is a bridging molecule equivalent to TIN2 in human shelterin, which links the Taz1-Rap1 and the Pot1-Tpz1-Ccq1 sub-complexes, respectively bound to double- and single-stranded DNA at telomeres. Poz1 is required for the regulation of telomerase activity, and it has been hypothesised that it might do so by playing a structural role in the switching of telomeres from an open to a closed state. In this study, a reverse-2-hybrid approach was used to generate Poz1 alleles unable to interact with Rap1 or Tpz1 specifically. These alleles were subjected to phenotypic and biochemical analysis which indicated that neither individual interaction is sufficient to maintain telomere homeostasis. With telomere lengths similar to a Poz1 deletion, it is proposed that negative regulation cannot occur without the ability to form a closed complex. Given that Cdc13 is currently the only missing component in fission yeast, a second study was initiated aiming to identify a homologue by yeast-2-hybrid screening of a cDNA library, using Stn1 and Ten1 as baits. However, this approach did not yield any positive candidates. In an alternative approach, Stn1 temperature-sensitive (ts) alleles were generated and characterised. These were used to screen a genomic library for suppressors of the Stn1 ts phenotype. Several candidates were identified that require further examination while the ts allele analysis indicated that telomeres are lost in their entirety at non-permissive temperatures and that survivors of this process did so by chromosome circularisation, similar to Pot1 mutants.

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Sreedharan, Pillai Sreerekha. "Insight into Stc1-interactions bridging RNAi and chromatin modification in Schizosaccharomyces pombe." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28733.

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Compact heterochromatin is essential for genome stability and hence cell survival. Studies in many organisms including humans underline the importance of pericentromeric heterochromatin in centromere function. Fission yeast centromeres share a common structural organisation with those of their metazoan counterparts. The fission yeast model has been pivotal in understanding many key events in the pathway leading to the assembly of pericentromeric heterochromatin. In particular, studies in this system have revealed that the RNA interference (RNAi) pathway connects with the chromatin modification machinery to impart proper heterochromatin formation. Transcription of the pericentromeres by RNA polymerase II (Pol II) produces double stranded RNA (ds RNA) which is processed by Dicer(Dcr1) into small interfering RNAs (siRNAs). These siRNAs are loaded onto the Argonaute protein Ago1, and target the Ago1- containing RITS (RNA-Induced Transcriptional Silencing) complex to the pericentromeres via complementary base-pairing of the siRNA to the nascent centromeric transcript. RITS then recruits the sole Histone H3-K9-methyl transferase, Clr4, as part of the Clr4-complex, CLRC. The resulting H3K9-methyl marks further result in the recruitment of downstream chromatin binding proteins including the HP1- homolgue Swi6 which plays a key role in cohesin retention. Additionally, the H3K9- methyl marks are required for stabilising the association of CLRC and RITS, thereby promoting a reinforcing loop within the RNAi-mediated heterochromatin pathway. Thus crosstalk between RITS and CLRC is important in establishing and maintaining silent chromatin at the pericentromeres. Stc1 has been proposed to act as a critical link that connects the RITS and CLRC complexes. Stc1 is required for heterochromatin establishment and maintenance at the pericentromere and association of RITS with CLRC is lost in the absence of Stc1. Moreover, Stc1 directly interacts with Ago1 and is essential for siRNA production. These and other previous observations (Bayne et al. 2010) highlight the key role played by Stc1 in the RNAi-mediated heterochromatin pathway. To understand how Stc1 mediates the specific cross-talk between RNAi and chromatin modification, I have investigated the nature of Stc1 interactions with the RNAi and chromatin modification machineries. Using in-vitro binding assays, I found that Stc1 directly interacts with the CLRC subunits Dos2 and Clr4. I also identified the RITS subunit Tas3 as a potential interactor of Stc1, in addition to Ago1. A collaborating research group elucidated the structure of Stc1 using NMR (He et al. 2013) and my study provides evidence for interactions via the distinct domains of Stc1. Stc1 utilises its disordered C-terminus to bind to Dos2 while the N-terminus, which contains a tandem zinc finger domain, acts as a multi-protein interaction interface binding the CLRC subunit Clr4 and RITS subunits Ago1 and Tas3, opening up possibilities for Stc1-containing distinct-complexes. My work provides new insights into the role of Stc1 and opens up future avenues of research key to understanding how heterochromatin domains are defined and maintained.

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Monteros, Juan Carlos. "Conservação evolutiva da proteína STI1 nas espécies Mus musculus e Danio rerio." reponame:Repositório Institucional da UFPR, 2009. http://hdl.handle.net/1884/20677.

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Cao, Hang [Verfasser]. "Effect of STIM1/2 and of Ceritinib on Platelet Function / Hang Cao." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1234450763/34.

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47

Frappier, Maude. "MURC est un partenaire d’interaction de STIM1 impliqué dans la signalisation calcique." Mémoire, Université de Sherbrooke, 2015. http://hdl.handle.net/11143/8332.

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Abstract:

Dans les cardiomyocytes, la concentration intracellulaire de Ca2+ doit être finement régulée pour maintenir l’homéostasie calcique. La protéine Stromal interaction molecule 1 (STIM1), qui joue un rôle important dans le maintien des niveaux intracellulaires de Ca2+ des cellules non excitables en opérant l’entrée capacitative de Ca2+ (SOCE), est aussi présente dans les cardiomyocytes. Plusieurs études démontrent que STIM1 et le SOCE jouent un rôle important dans le développement de l’hypertrophie des cardiomyocytes. De plus, récemment, un nouveau rôle de STIM1 a commencé à émerger. STIM1 pourrait moduler l’expression de certains canaux calciques à la membrane plasmique en régulant leur trafic intracellulaire. Le but de l’étude était d’identifier des partenaires d’interaction de STIM1 dans l’optique de révéler le mécanisme par lequel STIM1 induit l’internalisation d’un canal calcique voltage-dépendant. Les protéines recueillies par le pull-down à partir des lysats de coeurs de rats avec une colonne d’affinité composée du domaine ERM de STIM1, ont été analysées en spectrométrie de masse. La protéine Muscle related coiled-coil (MURC), une protéine de la famille des Cavin, a été retenue comme partenaire d’interaction potentiel de STIM1. Comme elle est exprimée dans les cardiomyocytes et dans les cellules musculaires squelettiques, qui sont des cellules où la régulation de la signalisation calcique est primordiale pour le bon fonctionnement des tissus et qu’elle semble interagir avec STIM1, qui est un acteur important de la signalisation calcique, notre objectif s’est élargi et nous avons investigué sur l’implication de MURC dans la signalisation calcique en général. Nous avons donc confirmé par co-immunoprécipitation que le domaine ERM de STIM1 interagissait avec MURC. Puis, par des essais d’imagerie calcique, nous avons démontré que la surexpression de MURC pouvait provoquer différentes réponses dans différents types cellulaires en fonction de l’activation de la mobilisation calcique. En effet, nous avons observé une augmentation du SOCE qui est indépendante de la voie RhoA/ROCK dans les cellules HEK293T, une diminution de l’entrée de calcium médiée par un récepteur (ROCE) qui est pourrait être dépendante de la voie RhoA/ROCK dans les cellules T6.11 et une diminution de l’activation de RhoA de façon dépendante de l’activation du SOCE dans les cardiomyocytes HL-1. Nous avons aussi montré que MURC pouvait interagir à la membrane plasmique avec les protéines Orai1, qui sont les protéines formant les canaux CRAC (Ca2+ release-activated Ca2+) du SOCE et ce de façon dépendante de l’activation de STIM1. Enfin, les résultats de cette étude suggèrent que MURC est un partenaire d’interaction de STIM1 impliqué dans la signalisation calcique. En effet, MURC peut moduler l’activation de RhoA, ce qui pourrait induire l’internalisation de canaux calciques. De plus, son interaction avec STIM1 et Orai1 pourrait notamment faire un pont facilitant l’interaction entre STIM1 et Orai1 ce qui aurait pour effet d’augmenter le SOCE et possiblement contribuer à augmenter l’hypertrophie des cardiomyocytes.

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48

Olthoff, Silke. "High temperature scanning tunnelling microscopy of adsorbate induced phase transitions." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264547.

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49

吳誼暉 and Yee-fai Ng. "Optimization of etching parameters for STM tips and an STM study of SiC (0001) [square root]3 x [square root]3 reconstruction." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B29797834.

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Ng, Yee-fai. "Optimization of etching parameters for STM tips and an STM study of SiC (0001) [square root]3 x [square root]3 reconstruction /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20567583.

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Dissertations / Theses on the topic 'STM1'

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