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Magi, Ross. "Dynamic behavior of biological membranes." Thesis, The University of Utah, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3680576.
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Biological membranes are important structural units in the cell. Composed of a lipid bilayer with embedded proteins, most exploration of membranes has focused on the proteins. While proteins play a vital role in membrane function, the lipids themselves can behave in dynamic ways which affect membrane structure and function. Furthermore, the dynamic behavior of the lipids can affect and be affected by membrane geometry. A novel fluid membrane model is developed in which two different types of lipids flow in a deforming membrane, modelled as a two-dimensional Riemannian manifold that resists bending. The two lipids behave like viscous Newtonian fluids whose motion is determined by realistic physical forces. By examining the stability of various shapes, it is shown that instability may result if the two lipids forming the membrane possess biophysical qualities, which cause them to respond differently to membrane curvature. By means of numerical simulation of a simplified model, it is shown that this instability results in curvature induced phase separation. Applying the simplified model to the Golgi apparatus, it is hypothesized that curvature induced phase separation may occur in a Golgi cisterna, aiding in the process of protein sorting.
In addition to flowing tangentially in the membrane, lipids also flip back and forth between the two leaflets in the bilayer. While traditionally assumed to occur very slowly, recent experiments have indicated that lipid flip-flop may occur rapidly. Two models are developed that explore the effect of rapid flip-flop on membrane geometry and the effect of a pH gradient on the distribution of charged lipids in the leaflets of the bilayer. By means of a stochastic model, it is shown that even the rapid flip-flop rates observed are unlikely to be significant inducers of membrane curvature. By means of a nonlinear Poisson- Boltzmann model, it is shown that pH gradients are unlikely to be significant inducers of bilayer asymmetry under physiological conditions.
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Waheed, Qaiser. "Molecular Dynamic Simulations of Biological Membranes." Doctoral thesis, KTH, Teoretisk biologisk fysik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-102268.
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Biological membranes mainly constituent lipid molecules along with some proteins and steroles. The properties of the pure lipid bilayers as well as in the presence of other constituents (in case of two or three component systems) are very important to be studied carefully to model these systems and compare them with the realistic systems. Molecular dynamic simulations provide a good opportunity to model such systems and to study them at microscopic level where experiments fail to do. In this thesis we study the structural and dynamic properties of the pure phospholipid bilayers and the phase behavior of phospholipid bilayers when other constituents are present in them. Material and structural properties like area per lipid and area compressibility of the phospholipids show a big scatter in experiments. These properties are studied for different system sizes and it was found that the increasing undulations in large systems effect these properties. A correction was applied to area per lipid and area compressibility using the Helfrich theory in Fourier space. Other structural properties like order of the lipid chains, electron density and radial distribution functions are calculated which give the structure of the lipid bilayer along the normal and in the lateral direction. These properties are compared to the X-ray and neutron scattering experiments after Fourier transform. Thermodynamic properties like heat capacity and heat of melting are also calculated from derivatives of energies available in molecular dynamics. Heat capacity on the other hand include quantum effect and are corrected for that by applying quantum correction using normal mode analysis for a simple as well as ambiguous system like water. Here it is done for SPC/E water model. The purpose of this study is to further apply the quantum corrections on macromolecules like lipids by using this technique. Furthermore the phase behavior of two component systems (phospholipids/cholesterol) is also studied. Phase transition in these systems is observed at different cholesterol concentrations as a function of temperature by looking at different quantities (as an order parameter) like the order of chains, area per molecule and partial specific area. Radial distribution functions are used to look at the in plane structure for different phases having a different lateral or positional order. Adding more cholesterol orders the lipid chains changing a liquid disordered system into a liquid ordered one and turning a solid ordered system into a liquid ordered one. Further more the free energy of domain formation is calculated to investigate the two phasecoexistence in binary systems. Free energy contains two terms. One is bulk freeenergy which was calculated by the chemical potential of cholesterol moleculein a homogeneous system which is favorable for segregation. Second is thefree energy of having an interface which is calculated from the line tension of the interface of two systems with different cholesterol concentration which in unfavorable for domain formation. The size of the domains calculated from these two contributions to the free energy gives the domains of a few nm in size. Though we could not find any such domains by directly looking at our simulations.QC 20120913
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Turkson, Abraham K. "Electro-ultrafiltration with rotating dynamic membranes." Thesis, McGill University, 1985. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=72036.
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In axial electrofiltration, a DC electric field is imposed between a rotating inner cylinder and a stationary outer cylinder giving rise to four mechanisms which act to minimize solute accumulation at the filter surface: turbulence, centrifugal force, electrophoresis and shear stress which removes solute aggregates.Four dynamic membranes, Zr(IV) oxide, calcium oleate, poly-2-vinylpyridine and cadmium sulfide, were used to filter bovine serum albumin (BSA) in a disodium phosphate solution at pH = 8 and Prussian blue in distilled water. Prussian blue is a particle of 0.01(mu)m diameter with a zeta potential of -41mV while BSA is a macromolecule of 69,000 molecular weight, a Stokes-Einstein radius of 0.0038(mu)m and a zeta potential of -23.3mV at pH = 8. For BSA, the flux declined with time while the rejection increased. Filtrate fluxes increased with rotation rate and electric field and declined with concentration for both feeds. The flux declined beyond N = 2000rpm and was constant above C(,0) = 5.0wt%. For Prussian blue, the rejection was greater than 90% at all levels of E, N and C(,0). For BSA, the rejection increased with rotation rate and declined with concentration. The BSA rejection declined above N = 2000rpm and was constant beyond C(,0) = 0.5wt%.
A mathematical model was derived to predict the time variation of filtrate flux and a rejection model was used to predict the effect of surface concentration on BSA rejection.
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Ip, Anita Wai Ching Chemical Sciences & Engineering Faculty of Engineering UNSW. "Dynamic membranes: formation and characterisation studies." Awarded by:University of New South Wales, 2005. http://handle.unsw.edu.au/1959.4/37836.
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Dynamic membranes are considered to be an attractive anti-fouling remedy for membrane filtration, because once fouled, they can be removed and reformed in-situ, thereby prolonging the support membrane???s lifetime. However, large-scale application of dynamic membranes has been limited due to the numerous formation parameters that influence their properties. This thesis provides better understanding of the mechanisms of the dynamic membrane formation process through fundamental formation and characterisation studies of dynamically formed titanium dioxide membranes in laboratory scale dead-end and crossflow systems. The dynamic membranes exhibited water fluxes ranging from 30-1147 L/m2h and dextran (500 kDa) rejections as high as 99.9%. Of the six formation parameters studied, the pH and constant flux conditions had the greatest influence on dynamic membrane properties. The pH affects dynamic membrane properties by changing particle aggregation prior to dynamic membrane formation, while constant flux conditions affect the drag force on particles during deposition thereby altering cake compressibility. The advantage of using the novel concept of constant flux formation over traditional constant pressure formation is that it enables greater control of particle deposition during dynamic membrane formation. Dextran rejection data also suggested the existence of a critical mass loading, above which dynamic membrane flux and rejection properties are reduced. This thesis also demonstrated the utility of a factorial design experiment for preliminary identification and evaluation of the critical factors affecting dynamic membrane formation, a method which could be invaluable for tailoring dynamic membranes for use in specific applications. In addition, cake removal data suggested that more than 80% of the dried cake could be removed providing a high potential for membrane regeneration. For the formation conditions studied, it was concluded that convection was the dominant mechanism governing particle transport during dynamic membrane formation. The fluxes and cake properties of the dynamic membranes were best described by the resistance-in-series model for simple dead-end microfiltration. Furthermore, the higher cake void fraction required to fit the experimental data (at low formation pressure or constant flux conditions) with model predictions suggested that the ratio of shear to convection was an important mechanistic parameter determining dynamic membrane properties.
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SOARES, RENATA MACHADO. "DYNAMIC ANALYSIS OF HYPERLASTIC CIRCULAR MEMBRANES." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2009. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=13790@1.
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PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIROCOORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO
FUNDAÇÃO DE APOIO À PESQUISA DO ESTADO DO RIO DE JANEIRO
Nesta tese são estudadas as vibrações não-lineares de membranas circulares inicialmente tracionadas sujeitas a deformações finitas. O material da membrana é modelado como um material hiperelástico neo-Hookeano, isotrópico e incompressível. Baseada na teoria de deformações finitas para membranas hiperelásticas, uma formulação variacional é desenvolvida. Primeiro a solução da membrana sob tração radial uniforme é obtida e então as equações de movimento da membrana são obtidas pelo princípio de Hamilton. A partir das equações linearizadas, as freqüências e os modos de vibração da membrana são obtidos analiticamente. Os modos naturais são usados para aproximar o campo de deformações não-linear usando o método de Galerkin e modelos de ordem reduzida são deduzidos através do método de Karhunen-Loève e de métodos analíticos. Além disso, estuda-se a influência da variação da massa específica e da espessura ao longo da direção radial da membrana nas vibrações. A seguir a mesma metodologia é utilizada para uma membrana anular. Por fim, estudam-se as vibrações não-lineares da membrana anular acoplada a uma inclusão rígida que insere tensões de tração na membrana, pois, devido ao seu peso próprio, provoca deslocamentos estáticos transversais e axissimétricos na membrana. Os mesmos problemas são analisados por elementos finitos utilizando o programa comercial Abaqus.
This work presents an analysis of the nonlinear vibration response of a prestretched hyperelastic circular membrane subjected to finite deformations. The membrane material is assumed to be isotropic, homogeneous and neo-Hookean. Based on the theory of finite deformations for hyperelastic membranes, a variational formulation is developed. First the exact solution of the membrane under a uniform radial stretch is obtained and then the equations of motion of the pre-stretched membrane are derived using the Hamilton’s principle. From the linearized equations of motion, the natural frequencies and mode shapes of the membrane are obtained analytically. Then the natural modes are used to approximate the nonlinear deformation field using the Galerkin method. Several reduced order models are tested using the Karhunen-Loève method and analytical methods. Besides, the influence of the variation of the membrane thickness and material density along the radial direction of the membrane on the vibrations is investigated. The same methodology it is used for the annular membrane. Finally, the non-linear vibrations of the annular membrane coupled to a rigid inclusion are studied. The rigid inclusion inserts traction forces in the membrane and its own weight causes static transverse and radial displacements in the membrane. The same problems are analyzed by finite elements using the commercial program Abaqus®.
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McCarthy, Nicola L. C. "Imaging dynamic patterning in lipid membranes." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/44075.
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Lateral inhomogeneity in biological membranes has been linked with many cellular functionalities including protein sorting and signal transduction. Fluid phase coexistence has been extensively studied by modelling membranes as bulk mesophases and as giant unilamellar vesicles (GUVs). However, the basis for microdomain formation in cells remains uncertain, and this is thought to be due to the small domain size and the highly dynamic nature of the cell membrane. The application of high pressure technology offers an ideal biophysical tool for the study of phase behaviour in model membranes both in and out of equilibrium. By coupling high-pressure technology with fluorescence microscopy we have been able to simultaneously induce and visualize phase separation in GUVs. This allows the structural dynamics (including domain size and morphology in individual vesicles) to be studied, which ideally compliments small angle x-ray scattering (SAXS) measurements of bulk mesophase properties. We employ high pressure technology to induce thickness mismatch and therefore alter the line tension between coexisting liquid domains, and to study the pressure effects on the lateral structuring of membranes containing general anaesthetics. The ability to trigger rapid phase separation using pressure-jumps across the phase boundary has been used to study the dynamic evolution of structural changes, with time-resolved microscopy and SAXS giving an insight into transition kinetics, energetics and mechanisms.
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Nandurkar, Kuldeep Pandurang. "Static and Dynamic Behavior of Stress Coated Membranes." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/nandurkar/NandurkarK0806.pdf.
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Large space mirrors need to be made of ultra-lightweight materials (membranes) that have very low densities and high flexibility (compliance) for packaging. A coating application necessary for optical reflectivity may also impart to these ultra-lightweight materials a desired shape and to help maintain that shape in the harsh environment of space. When a coating is applied on the membrane substrate, stresses develop in the coating due to atomistic processes. These stresses are fundamental to the final shape of the substrate. Coatings applied to the substrate in order to maintain a particular shape are known as the 'stress coating prescription'. As there is no way one could directly measure stresses in the coatings experimentally, in this work it will be explained how finite element analysis (FEA) was used in estimating stresses in the coatings. This work mainly comprises static pressuredeflection tests (bulge tests) on the coated and uncoated membranes, and a comparison of the experimental results to FEA findings in order to estimate the stresses in the coatings. Before FEA results are matched with the experimental results, an analytical solution to the problem in hand will be derived. Uncertainties due to variation in coating thicknesses and difficulties in coating process have led to various uncertainties in this work, and these uncertainties are also discussed. The ability to use changes in vibration frequency as a measure of coating stress is also investigated.
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Al-Malack, Muhammad Hassan. "Applications of dynamic membranes to crossflow microfiltration of secondary effluent." Thesis, University of Newcastle Upon Tyne, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335944.
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Thurmond, Robin Leroy. "Average and dynamic properties of membrane lipids studied by deuterium NMR spectroscopy." Diss., The University of Arizona, 1992. http://hdl.handle.net/10150/185835.
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If the function of membrane lipids were only to provide a permeability barrier for cells, than a single lipid species such as phosphatidylcholine would suffice since it would maintain the bilayer structure necessary for a membrane. Cells, however, go out of their way to regulate the components of their membranes and therefore there must be some reason for the vast diversity of lipids found even in a single membrane. Modulation of the phospholipid composition could affect both the average and dynamical properties of the entire system. Average properties such as the hydrocarbon thickness, the area per lipid molecule, or the curvature stress across the bilayer could play a role in membrane function and therefore it is important to understand how different lipid components influence these physical properties. The goal of this work has been to understand how different lipid components such as changes in headgroup and acyl chain unsaturation as well as cholesterol and bile salts affect the properties and structure of membranes through the use of deuterium nuclear magnetic resonance spectroscopy (²H NMR). Saturated and unsaturated phosphatidylethanolamines and phosphatidylcholines have been studied in the low temperature, lamellar liquid-crystalline, and reversed hexagonal phases. Measurements have been made of the average projected acyl chain length, the average area per molecule, the radius of curvature in hexagonal phases, and various relaxation rates. These studies were not only carried out on single component synthetic systems but also mixture of lipids and even native membranes through the use of a deuterated probe molecule. It was concluded that different lipids modulate different properties of membranes. Phosphatidylcholines along with monounsaturation keep the membranes in a fluid state whereas the presence of phosphatidylethanolamines and polyunsaturation increase the curvature stress in the monolayers. With this in mind experiments were carried out to determine how the average properties of membranes relate to membrane protein function. These studies show the promise of combining physical chemical measurements of membrane properties with biochemical measures of protein function. Such studies will allow for a better understanding of membrane function and the role lipid diversity plays in such functions.
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Saggiomo, Vittorio [Verfasser]. "Ion transport across membranes mediated by a dynamic combinatorial library / Vittorio Saggiomo." Kiel : Universitätsbibliothek Kiel, 2010. http://d-nb.info/1019984619/34.
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Winkler, Pamina M. "Novel planar photonic antennas to address the dynamic nanoarchitecture of biological membranes." Doctoral thesis, Universitat Politècnica de Catalunya, 2020. http://hdl.handle.net/10803/670293.
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The cell membrane is the encompassing protective shield of every cell and it is composed of a multitude of proteins, lipids and other molecules. The organization of the cell membrane is inextricably intertwined with its function, and sensitive to perturbations from the underlying actin cytoskeleton and the extracellular environment at the nano- and the mesoscale. Elucidating the dynamic interplay between lipids and proteins diffusing on the cell membrane, forming transient domains and (re)organizing them according to signals from the juxtaposed inner and outer meshwork, is of paramount interest in fundamental cell biology. The overarching goal of this thesis is to gain deeper insight into how lipids and proteins dynamically organize in biological membranes at the nanoscale.
Photonic nano-antennas are metallic nanostructures that localize and enhance the incident optical radiation into highly confined nanometric regions (< 20 nm), leading to greatly enhanced light-matter interactions. In this thesis, we exploit an innovative design of planar gold nano-antenna arrays of different gap sizes (10-45 nm) and embedded in nanometric-size boxes. To elucidate nanoscale diffusion dynamics in biological membranes with high spatiotemporal resolution and single-molecule detection sensitivity, we further combine our nanogap antenna arrays with fluorescence correlation spectroscopy (FCS) in a serial and multiplexed manner.
In this dissertation, we first describe the fabrication process of these planar gold nanogap antennas and characterize their performance by means of electron microscopy and FCS of individual molecules in solution. We demonstrate giant fluorescence enhancement factors of up to 104-105 times provided by our planar nanogap antennas in ultra-confined detection volumes and with single molecule detection sensitivity in the micromolar range.
Second, we apply these planar plasmonic nano-antennas in combination with FCS for assessing the dynamic organization of mimetic lipid membranes at the nanoscale. For a ternary composition of the model membranes that include unsaturated and saturated lipids together with cholesterol, we resolve transient nanoscopic heterogeneities as small as 10 nm in size, coexisting in both macroscopically phase-separated lipid phases.
Third, we add a Hyaluronic Acid (HA) layer on top of the model lipid membranes to emulate the effect of the extracellular environment surrounding native biological membranes. We extend our nano-antenna-FCS approach with atomic force microscopy and spectroscopy. We reveal a distinct influence of HA on the nanoscale lipid organization of mimetic membranes composed of lipids constituting the more ordered lipid phase. Our results indicate a synergistic effect of cholesterol and HA re-organizing biological membranes at the nanoscale.
Fourth, we apply our planar nano-antenna platform combined with FCS to elucidate the nanoscale dynamics of different lipids in living cells. With our nanogap antennas we were able to breach into the sub-30 nm spatial scale on living cell membranes for the first time. We provide compelling evidence of short-lived cholesterol-induced ~10 nm nanodomain partitioning in living plasma membranes.
Fifth, we demonstrate the multiplexing capabilities of our planar gold nanogap antenna platform combined with FCS in a widefield illumination scheme combined with sCMOS camera detection. Our approach allows recording of fluorescence signal from more than 200 antennas simultaneously. Moreover, we demonstrate multiplexed FCS recording on 50 nano-antennas simultaneously, both in solution as well as in living cells, with a temporal resolution in the millisecond range. The dissertation finishes with a brief discussion of the main results achieved in this research and proposes new avenues for future research in the field.La membrana plasmática separa el entorno intracelular del extracelular y está compuesta por una multitud de diferentes proteínas y lípidos. Su organización está fuertemente interconectada a su función, y es sensible a perturbaciones tanto de la actina cortical posicionada internamente en proximidad con la membrana, así como de una red extracelular en contacto próximo con la membrana exterior. Estas perturbaciones ocurren a distintas escalas temporales y espaciales, llegando a unos pocos nanómetros. Dada la estrecha relación entre la organización de la membrana y su función biológica, es tremendamente importante entender como lípidos y proteínas se organizan dinámicamente a la escala nanométrica y como se ven afectados por su entorno. El objetivo principal de esta tesis doctoral se centra en alcanzar este entendimiento. Las antenas fotónicas son nano-estructuras metálicas que incrementan la radiación electromagnética en regiones nanométricas (< 20 nm) del espacio. En esta tesis doctoral, hemos fabricado y utilizado plataformas con matrices de antenas en oro, y con regiones de confinamiento entre 10-45 nm. Además, hemos combinado estas antenas con la técnica de ¿fluorescence correlation spectroscopy (FCS)¿ a fin de obtener información espaciotemporal a la nano-escala en membranas biológicas, junto a la sensibilidad de detectar moléculas individuales a altas concentraciones. En esta disertación, describimos primero la fabricación de antenas fotónicas y caracterizamos su rendimiento utilizando técnicas de microscopía electrónica y FCS de moléculas individuales en solución. Nuestros resultados demuestran factores de incremento de la fluorescencia entre 104-105, en regiones ultra-confinadas, y una capacidad para detectar moléculas individuales en rango de concentraciones de micro-molares. Una vez validadas nuestras herramientas, nos enfocamos en su uso para el estudio dinámico de la organización de membranas lipídicas miméticas a escala nanométrica. En el caso de composiciones ternarias de lípidos insaturados, saturados y colesterol, hemos descubierto la existencia de heterogeneidades nanoscópicas y transitorias que coexisten tanto en las regiones ordenadas como desordenadas de las membranas lipídicas. El siguiente capítulo contiene resultados enfocados a estudiar el efecto del entorno extracelular en la organización dinámica de este tipo de capas lipídicas. Para ello, y como modelo, preparamos membranas lipídicas cubiertas de ácido hialurónico (HA), un componente abundantemente expresado en la matriz extracelular. Combinando FCS con microscopia y espectroscopia de fuerzas atómicas, logramos resolver la influencia de HA a escala nanométrica en la organización de la fase ordenada de las membranas lipídicas. Nuestros resultados indican la existencia de un efecto sinérgico entre HA y colesterol en el reordenamiento de la membrana a la nano-escala. El siguiente tema de investigación en esta tesis doctoral se enfoca a la aplicación de antenas fotónicas y FCS para el estudio de dominios lipídicos enriquecidos de colesterol en la membrana plasmática de células vivas. La utilización de estas antenas nos ha permitido, por primera vez, remontar la barrera de 30 nm, y demostrar de manera inequívoca la existencia de dominios enriquecidos en colesterol en células vivas con una resolución espacial de 10 nm. Finalmente, hemos demostrado la capacidad de multiplexado de nuestras antenas fotónicas, combinando una iluminación y detección en campo amplio utilizando una camera sCMOS. Describimos la implementación de nuestro esquema, así como también medidas que demuestran la detección simultánea de fluorescencia en más de 200 antenas. De manera importante, demostramos la obtención de curvas de FCS en 50 antenas simultáneamente, tanto en solución como en células vivas. Esta disertación culmina con una breve discusión de los resultados más importantes de esta investigación en el futuro
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Mahon, Eugene. "Dynamic Constitutional Protein-Carbohydrate and Polyoxometalate Systems toward biomimetic sensors and membranes." Montpellier 2, 2009. http://www.theses.fr/2009MON20057.
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Le but de ce travail était d'explorer l'interaction entre les ensembles supramoléculaires constitutionnels et chimie dynamiques biomimétique et les motifs biologiques simples. La recherche a été effectuée dans les domaines d'intérêt suivants : l'interaction protéine-saccharides, les vésicules, les bicouches phospholipidiques, les canaux ioniques et le transport à travers une membrane et ont constituer trois axes de projet. Des nanoparticules ont été employée pour l'amplification de signal de fréquence d'une microbalance à cristal de quartz pour la recherche sur l'interaction de lectin-saccharide montrant une haute spécificité et une augmentation d'affinité par multivalence. Polyoxomolydates, nanoarchitectures qui possèdent le potentiel de former les canaux ioniques biomimetiques ont montrés que'ils s'incorporaient spontanément dans les bicouches lipidique cela facilitait les flux des cations. De plus ces nanoclusters anioniques ont démontré une organisation électrostatique sur des bicouches lipidiques qui peuvent être appliqué au développement de matériaux hybrides et aussi les études des propriétés médicinales des polyoxomolybdates. Pour finir une membrane liquide supporté contenant une lectin Concanavalin A dans une nanoemulsion a été développé pour étudier le transport d'une bibliothèque combinatoire dynamique simpleThe aim of this work was to explore the interaction between biomimetic supramolecular and dynamic constitutional chemistry ensembles and simple biological motifs. Research was performed in the following areas of interest: carbohydrate-protein interaction, vesicles, bilayers, ion channels and membrane transport constituting three projects. Quartz crystal microbalance measurement was coupled with nanoparticle mass amplification for investigation of lectin-carbohydrate interaction showing high specificity and affinity enhancement through multivalency. Polyoxomolydates, nanoarchitectures which possess the potential to form biomimetic ion channels were shown to spontaneously partition in lipid bilayers and mediate cation flux, additionally theses anionic nanoclusters demonstrated electrostatic organisation on lipid bilayers which can be applied in hybrid material development and investigation the demonstrated medicinal properties of polyoxomolybdates. Lastly a lectin occluding supported liquid membrane was developed to investigate transport of a simple dynamic combinatorial library
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Fox, Jason William. "Electromechanical Characterization of the Static and Dynamic Response of Dielectric Elastomer Membranes." Thesis, Virginia Tech, 2007. http://hdl.handle.net/10919/34909.
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Dielectric elastomers (DEs) are a relatively new electroactive polymer (EAP) transducer technology. They are capable of over 100% strain when actuated, and can be used as sensors to measure large strains. In actuation mode, the DE is subject to an electric field; in sensing mode, the capacitance of the dielectric elastomer is measured. In this work, a dielectric elastomer configured as a circular membrane clamped around its outer edge over a sealed chamber and inflated by a bias pressure is studied in order to characterize its static and dynamic electromechanical behavior. In both cases, the experiments were conducted with prestretched dielectric elastomer actuators fabricated from 0.5 mm or 1 mm thick polyacrylate films and unless stated otherwise carbon grease electrodes were used.
The static tests investigate the effect of flexible electrodes and passive layers on the electromechanical response of dielectric elastomer membrane actuators and sensors. To study the effect of the flexible electrodes, four compliant electrodes were tested: carbon grease, silver grease, graphite spray, and graphite powder. The electrode experiments show that carbon grease is the most effective electrode of those tested. To protect the flexible electrodes from environmental hazards, the effect of adding passive elastic layers to the transducers was investigated. A series of tests were conducted whereby the position of the added layers relative to the transducer was varied: (i) top passive layer, (ii) bottom passive layer, and (iii) passive layers on both the bottom and top of the transducer. For the passive layer tests, the results show that adding elastic layers made of the same material as the DE dramatically changes both the mechanical and electrical response of the actuator. The ability to use capacitance measurements to determine the membraneâ s maximum stretch was also investigated. The experiments demonstrate that the capacitance response can be used to sense large mechanical strains in the membrane ï ³ 25%. In addition, a numerical model was developed which correlates very well with the experimental results especially for strains up to 41%.
The dynamic experiments investigate the dynamic response of a dielectric elastomer membrane due to (i) a time-varying pressure input and (ii) a time-varying voltage input. For the time-varying pressure experiments, the prestretched membrane was inflated and deflated mechanically while a constant voltage was applied. The membrane was cycled between various predetermined inflation states, the largest of which was nearly hemispherical, which with an applied constant voltage of 3 kV corresponded to a maximum strain at the pole (center of membrane) of 28%. These experiments show that for higher voltages, the volume displaced by the membrane increases and the pressure inside the chamber decreases. For the time varying voltage experiments, the membrane was passively inflated to various predetermined states, and then actuated. Various experiments were conducted to see how varying certain system parameters changed the membraneâ s dynamic response. These included changing the chamber volume and voltage signal offset, as well as measuring the displacement of multiple points along the membraneâ s radius in order to capture its entire motion. The chamber volume experiments reveal that increasing the size of the chamber onto which the membrane is clamped will cause the resonance peaks to shift and change in number. For these experiments, the pole strains incurred during the inflation were as high as 26 %, corresponding to slightly less than a hemispherical state. Upon actuation using a voltage signal with an amplitude of 1.5 kV, the membrane would inflate further, causing a maximum additional strain of 12.1%. The voltage signal offset experiments show that adding offset to the input signal causes the membrane to oscillate at two distinct frequencies rather than one. Lastly, experiments to capture the entire motion of the membrane revealed the different mode shapes the membraneâ s motion resembles.Master of Science
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Dietrich, Undine. "Structural and dynamic studies of MARCKS interaction with PIP(2) containing lipid membranes." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-77727.
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MARCKS-Protein ist in den Signalübertragungsweg der Zelle involviert. Durch einen Adsorptions-/Desorptionszyklus mit der Zellmembran reguliert es die Konzentration bestimmter Botenmoleküle. Im Rahmen dieser Arbeit wurde untersucht, inwieweit strukturelle Änderungen der Membran, verursacht durch die Membran-Protein-Wechselwirkung, mit einem Reaktions-Diffusions-System korrelieren.
Die elektrostatische Wechselwirkung von MARCKS-Protein mit negativ geladenen
Membranlipiden geschieht an der inneren Seite der Zellmembran. Als Modellsystem
lässt sich dies mit einer monomolekularen Lipidschicht an der Wasser-Luft-Grenzfläche realisieren. Anhand von oberflächensensitiven Messungen konnte gezeigt werden, dass die Wechselwirkung von MARCKS mit negativ geladenen Membranlipiden und damit die Adsorption an der Membran, zu einer Änderung der Membrantopologie führt. Damit verbundenen ist auch der partielle Einbau von MARCKS in die Membran, was zu einem größeren molekularen Flächenbedarf führt. Dieser korreliert mit dem Anstieg des lateralen Drucks der Lipidmonoschicht bei konstanter Fläche. Die Desorption von MARCKS kann durch die Wechselwirkung mit PKC induziert werden, detektierbar durch die Reduktion des lateralen Drucks. Bei Vorhandensein eines Reservoirs an MARCKS und PKC oszilliert der laterale Druck, was als zyklische Adsorption und Desorption von MARCKS an bzw. von der Lipidschicht interpretiert wird. Anhand der experimentellen Ergebnisse wurde ein mathematisches Modell entwickelt, dass dieses oszillierende Verhalten als ein Reaktions-Diffusions-System erklärt.
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Kapoor, Hitesh. "Nonlinear Dynamic Response of Flexible Membrane Structures to Blast Loads." Thesis, Virginia Tech, 2005. http://hdl.handle.net/10919/41238.
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The present work describes the finite element (FE) modeling and dynamic response of lightweight, deployable shelters (tent) to large external blast loads. Flexible shelters have been used as temporary storage places for housing equipments, vehicles etc. TEMPER Tents, Small Shelter System have been widely used by Air Force and Army, for various field applications. These shelters have pressurized Collective Protection System (CPS), liner, fitted to the frame structure, which can provide protection against explosives and other harmful agents. Presently, these shelter systems are being tested for the force protection standards against the explosions like air-blast. In the field tests carried out by Air Force Research Laboratory, it was revealed that the liner fitted inside the tent was damaged due to the air blast explosion at some distant from the structure, with major damage being on the back side of the tent. The damage comprised of tearing of liner and separation of zip seals. To investigate the failure, a computational approach, due to its simplicity and ability to solve the complex problems, is used.
The response of any structural form to dynamic loading condition is very difficult to predict due to its dependence on multiple factors like the duration of the loading, peak load, shape of the pulse, the impulse energy, boundary conditions and material properties etc. And dynamic analysis of shell structures pose even much greater challenge. Obtaining solution analytically presents a very difficult preposition when nonlinearity is considered. Therefore, the numerical approach is sought which provide simplicity and comparable accuracy.
A 3D finite element model has been developed, consisting of fabric skin supported over the frames based on two approaches. ANSYS has been used for obtaining the dynamic response of shelter against the blast loads. In the first approach, the shell is considered as a membrane away from its boundaries, in which the stress couple is neglected in its interior region. In the second approach, stress coupling is neglected over the whole region. Three models were developed using Shell 63, Shell 181 and Shell 41. Shell 63 element supports both the membrane only and membrane-bending combined options and include stress stiffening and large deflection capabilities. Shell 181 include all these options as Shell 63 does and also, accounts for the follower loads. Shell 41 is a membrane element and does not include any bending stiffness. This element also include stress stiffening and large deflection capabilities.
A nonlinear static analysis is performed for a simple plate model using the elements, Shell 41 and Shell 63. The membrane dominated behavior is observed for the shell model as the pressure load is increased. It is also observed that the higher value of Young's modulus (E) increases the stresses significantly.
Transient analysis is a method of determining the structural response due to time dependent loading conditions. The full method has been used for performing the nonlinear transient analysis. Its more expensive in terms of computation involved but it takes into account all types of nonlinearities such as plasticity, large deflection and large strain etc. Implicit approach has been used where Newmark method along with the Newton-Raphson method has been used for the nonlinear analysis. Dynamic response comprising of displacement-time history and dynamic stresses has been obtained. From the displacement response, it is observed that the first movement of the back wall is out of the tent in contrast to the other sides whose first movement is into the tent. Dynamic stresses showed fluctuations in the region when the blast is acting on the structure and in the initial free vibration zone.
A parametric study is performed to provide insight into the design criteria. It is observed that the mass could be an effective means of reducing the peak responses. As the value of the Young's Modulus (E) is increased, the peak displacements are reduced resulting from the increase in stiffness. The increased stiffness lead to reduced transmitted peak pressure and reduced value of maximum strain. But a disproportionate increase lead to higher stresses which could result in failure. Therefore, a high modulus value should be avoided.Master of Science
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Longun, Jimmy. "Processing and Evaluation of Multifunctional Polyimide Composite Coatings and Membranes." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1367938249.
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Comer, Anthony C. "DYNAMIC RELAXATION PROPERTIES OF AROMATIC POLYIMIDES AND POLYMER NANOCOMPOSITES." UKnowledge, 2011. http://uknowledge.uky.edu/cme_etds/1.
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The dynamic relaxation characteristics of Matrimid® (BTDA-DAPI) polyimide and several functionalized aromatic polyimides have been investigated using dynamic mechanical and dielectric methods. The functionalized polyimides were thermally rearranged to generate polybenzoxazole membranes with controlled free volume characteristics. All polyimides have application in membrane separations and exhibit three motional processes with increasing temperature: two sub-glass relaxations (ƴ and β transitions), and the glass-rubber (α) transition. For Matrimid, the low-temperature ƴ transition is purely non-cooperative, while the β sub-glass transition shows a more cooperative character as assessed via the Starkweather method. For the thermally rearranged polyimides, the ƴ transition is a function of the polymer synthesis method, thermal history, and ambient moisture. The β relaxation shows a dual character with increasing thermal rearrangement, the emerging lower-temperature component reflecting motions encompassing a more compact backbone contour. For the glass-rubber (α) transition, dynamic mechanical studies reveal a strong shift in Tα to higher temperatures and a progressive reduction in relaxation intensity with increasing degree of thermal rearrangement.
The dynamic relaxation characteristics of poly(ether imide) and poly(methyl methacrylate) nanocomposites were investigated by dynamic mechanical analysis and dielectric spectroscopy. The nanoparticles used were native and surface-modified fumed silicas. The nanocomposites display a dual glass transition behavior encompassing a bulk polymer glass transition, and a second, higher-temperature transition reflecting relaxation of polymer chain segments constrained owing to their proximity to the particle surface. The position and intensity of the higher-temperature transition varies with particle loading and surface chemistry, and reflects the relative populations of segments constrained or immobilized at the particle-polymer interface. Dielectric measurements, which were used to probe the time-temperature response across the local sub-glass relaxations, indicate no variation in relaxation characteristics with particle loading.
Nanocomposite studies were also conducted on rubbery poly(ethylene oxide) networks crosslinked in the presence of MgO or SiO2 nanoparticles. The inclusion of nanoparticles led to a systematic increase in rubbery modulus and a modest positive offset in the measured glass transition temperature (Tα) for both systems. The sizeable increases in gas transport with particle loading reported for certain other rubbery nanocomposite systems were not realized in these crosslinked networks.
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Zarragoitia, Gonzalez Alain. "Développement de modèles dynamiques pour la simulation et l'optimisation de bioréacteurs à membranes immergées pour le traitement d'eaux usées." Thesis, Toulouse, INPT, 2009. http://www.theses.fr/2009INPT016G/document.
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Le traitement des effluents et eaux usées par bioréacteurs à membranes immergées (BAMI) permet d'obtenir une haute qualité de perméat par une dégradation biologique et une séparation physique. Néanmoins, le procédé de filtration est limité par l'influence de facteurs très complexes, en particulier le colmatage de la membrane. Le but du travail est de développer des modèles dynamiques et de simuler le procédé de filtration dans les BAMI. Le développement et la simulation des modèles ont été ciblés sur la description des rapports existants entre les variables les plus importantes du système, comme la pression transmembranaire (PTM), les matières en suspension (MES), les substances polymériques extracellulaires (SPE) et l'influence sur l'évolution du colmatage d'une aération syncopée, injectée à la surface de membrane, et sa synchronisation avec une filtration intermittente. Le modèle et les études d'optimisation du système ont été validé par voie expérimentaleThis thesis studies a submerged membrane bioreactor (MBR) technology that is used to treat effluents. We present in detail the modeling of this process, the validation of developed models, and the results of simulation and optimization carried out with the above mentioned models. The new contributions to scientific knowledge of this work are the following: - A new dynamic model that integrates for such systems, many of the variables and the main phenomena occurring during the process of filtration in MBR wastewater treatment. That constitutes an original contribution to the analysis and development of this technology. – The simulation allows to achieve the quantification of the influence and effect of aeration on the process (membranes fouling) and the influence of the sequencing of the filtration and coarse bubbles aeration cycles. All that takes into account the behavior of biomass, the generation of exopolymeric substances and inlet characteristics. The results provided by the model are validated by comparison with experimental results. – An optimization of MBR operating conditions using the experimental design for simulation, is reported based on the results obtained using the developed models
En la presente tesis se reflejan los estudios realizados en un biorreactor con membrana sumergida, tecnología que se utiliza para el tratamiento de efluentes residuales. Se presentan de forma detallada la modelación de este proceso, la validación de los modelos desarrollados, así como los resultados de la simulación y optimización realizados con los modelos. Entre los nuevos aportes al conocimiento científico del trabajo se encuentran los siguientes: - Un nuevo modelo dinámico que integra por primera vez, para estos sistemas, muchas de las variables y los principales fenómenos que ocurren durante el proceso de filtración y tratamiento de las aguas residuales utilizando los BMS. Lo cual constituye un aporte novedoso para el análisis y desarrollo de esta tecnología. - Se logró por primera vez cuantificar mediante simulación la influencia y el efecto de la aireación sobre el proceso de colmatación de las membranas, así como la influencia de la sincronización de los ciclos de filtración y aireación de burbujas gruesas. Todo esto tomando en cuenta el comportamiento de la biomasa, la generación de sustancias colmatantes y las características de la alimentación. Se validaron los resultados que ofrece el modelo mediante la comparación con resultados experimentales. - Se reporta por primera vez la optimización de las condiciones operacionales de un sistema BMS utilizando el diseño de experimento para la simulación, partiendo de los resultados obtenidos utilizando los modelos desarrollados
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Corre, Thomas. "Rupture dynamique de membranes élastomères : étude expérimentale par mesure de champs." Thesis, Ecole centrale de Nantes, 2018. http://www.theses.fr/2018ECDN0043/document.
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Cette thèse s’intéresse à la propagation dynamique de fissure dans les membranes élastomères du point de vue expérimental. Elle a pour but d’identifier les paramètres qui gouvernent la cinématique de ces fissures se propageant à grande vitesse, afin d’en prédire la trajectoire. Fondé sur l’utilisation conjointe d’une caméra à haute résolution et d’une caméra rapide, le dispositif expérimental permet de mesurer des champs à partir de la corrélation d’images au cours de la propagation de la fissure. Mis en pratique sur un polyuréthane, ce dispositif permet de retrouver la configuration de référence de l’éprouvette pendant la propagation de fissure, préalable indispensable à l’étude mécanique du problème. En plus des champs cinématiques, la densité d’énergie élastique et les contraintes sont évaluées grâce à une loi de comportement hypérélastique Les résultats de ces essais constituent une large base de données sur la rupture dynamique de membranes élastomères. La méthode permet de réaliser une analyse cinématique et énergétique de la propagation stationnaire et instationnaire, toujours dans la configuration de référence. La propagation supersonique est observée pour les hauts niveaux de déformation de la membrane. Enfin,ces observations permettent une discussion sur l’utilisation de l’approche énergétique de la rupture dynamique et de la pertinence des mesures de champs actuelles pour caractériser ce type de propagation de fissureThis PhD thesis tackles the issue of dynamic fracture of elastomer membranes from an experimental point of view. It aims at providing some insight to predict the trajectories of high speed cracks under large strain. An experimental procedure involving high resolution and high speed cameras is developed in order to perform full-field measurements based on digital image correlation during crack propagation. Tested with a highly stretchable elastomer (polyurethane), this set-up permits to retrieve the material configurations of the sample all along crack growth, which is a crucial step toward a complete mechanical analysis of the problem. In addition to the kinematic fields,both strain energy density and stress fields are estimated thanks to a hyperelastic model, which is issued from mechanical characterisation of the material. Results of these experiments provide a comprehensive database on dynamic fracture of membranes. The method is designed to perform kinematic and energetic analyses of both steady and unsteady crack propagation in the reference configuration. Supersonic crack growth is observed for large prescribed deformation of the membranes. Finally, these observations lead to a discussion on the energetic approach in dynamic crack growth and the current applicability of full-field measurements to characterise dynamic crack growth in elastomers
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Sarrouj, Hiba. "DNP/solid state NMR probehead for the investigation of oriented membranes." Phd thesis, Université de Strasbourg, 2014. http://tel.archives-ouvertes.fr/tel-01038015.
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Helical membrane proteins comprise one third of the expressed proteins encoded in a typical genome. Other membrane proteins are typically beta sheets. Their function varies from pore formation, signaling to antimicrobial activity. They are also capable of transporting large cargo such as proteins or nucleic acids across the cell membrane. Recently, peptides have emerged as promising tools in drug delivery. Membrane proteins can be synthesized chemically or expressed and isotopically labeled in bacteria, isolated, purified and reconstituted into fully hydrated lipid bilayers. The bilayer orientation is kept mechanically by putting them between glass plates. While interacting with these bilayers they exhibit a variety of configurations depending on the lipids composition and thickness. Solid-state Nuclear Magnetic Resonance (NMR) on oriented bilayers is one way to access the topology of peptides associated with phospholipid membranes. Oriented membrane protein are difficult to study with analytical techniques because of their poor solubility outside the lipid membrane, difficulty of expression in bacteria in big quantities, difficulty to crystallize, and they are too large for solution NMR study. The intensity of an NMR signal depends on several factors such as polarization P and magnetic field magnitude B0. One of the major drawbacks of NMR spectroscopy is low sensitivity. This is caused by the small magnetic moment of the nuclear spins which results in a modest Zeeman splitting of the nuclear spin energy levels and therefore in a limited Boltzmann Polarization. The aim of this project is to obtain a better signal from membrane proteins. Thus a Low temperature (LT) solid state NMR with Dynamic Nuclear Polarization (DNP) probe head was created. DNP is an ingenious technique that is used to transfer polarization from highly polarized targets to less polarized nuclei using microwave irradiation. Microwaves will excite selectively the electron spins which will transfer their polarization to the pool of proton nuclei, the proton NMR signal can be enhanced by 660 times. A probe head for DNP enhanced solid state NMR at 100 K and 9.4 T is described. A probe head includes the mechanical piece that holds the sample in the magnetic center of the NMR magnet. It is a tunable antenna that irradiates and detects the rf fields used in NMR. The centerpiece of the probe is the solenoidal or saddle coil surrounding the sample. The feasibility of such a DNP experiment is proven on magic angle oriented sample spinning. These experiments are conducted on oriented samples wrapped into a rotor. Through their orientation with regards to B0 is lost, enhancement values as high as 17 are obtained. [...]
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Günther, Jan. "Caractérisation et optimisation des phénomènes de transfert dans un double bioréacteur à membranes." Thesis, Toulouse, INPT, 2009. http://www.theses.fr/2009INPT047G/document.
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L'idée de base est de permettre à deux microorganismes de partager le même environnement tout en les maintenant séparées à l'aide d'une membrane perméable les retenant sélectivement. La principale contrainte résulte du transfert des composées d'intérêts limité par l'écoulement dans et autour des fibres ainsi que dans module et par le colmatage. Le double bioréacteur a membrane étudié dans cette thèse, de par son fonctionnement, alterne les cycles de filtration et rétrofiltration (ou rétrolavage), limitant ainsi en partie le colmatage. Ce travail de thèse s'est donc attaché à approfondir la connaissance des mécanismes de limitation au transfert mis en jeu lors de la filtration de fluide biologique complexes et évolutifs en fonction des conditions opératoires et des caractéristiques géométriques du module de filtration à fibres creuses. Dans cet objectif, sur la base des choix de configuration de module membranaire proposés dans cette étude, et afin de tendre vers une optimisation rationnelle de l'utilisation de ce dispositif, l'étude s'appuya sur l'utilisation d'outils de mécanique des fluides numériques, complétée par une approche expérimentale menée dans des conditions modèles. Les simulations réalisées par cette approche ont ainsi mis en évidence de grandes variations des vitesses de filtration le long de la fibre et ceci en lien direct avec une augmentation de la perte de charge à l'extérieur des fibres due au confinement induisant une baisse des performances de filtration. De manière similaire, un modèle numérique de formation de dépôt nous a permis d'évaluer l'effet du confinement de fibres. Il entraine une augmentation de pression dans la partie fluide externe induisant une forte variation de pertes de charges entrainant une répartition du dépôt le long de la fibre beaucoup plus inhomogène. Le retour du numérique à l'expérimental réalisé s'est attaché à décrire l'influence des conditions de mise oeuvre sur les performances de filtration du pilote. L'analyse méthodique de l'influence du sens de filtration et de la compacité dans le cas de fluides modèles (suspension de différents microorganismes / solutions de protéines modèles) et dans le cas de fluides biologiques évolutifs (milieux de fermentation + micro organismes) fut réalisée. L'ensemble de ces résultats nous permettent de donner des recommandations aux futurs utilisateurs du double bioréacteur à membranesThis work presents a specific bioreactor previously designed to study microbial interactions. In this process, the microbial species in two tanks are physically separated by a microfiltration membrane. In order to give to the microorganisms a molecular environment in each compartment similar to the one that would be obtained if the microbial cells were cultivated in the same reactor, two criteria have to be considered: (i) the flow rates between compartments have to be sufficient with respect to the microbial kinetics and (ii) all the molecular compounds of the medium that have an effect on the microorganism behaviour must pass through the membrane. The main constrain is due to transfer of component limited by the fluid flow in and around the fiber of the filtration module. This thesis has therefore committed to deepening the understanding of the mechanisms limiting the transfer involved during the filtration of biological fluid complex according to operating conditions and geometric characteristics of the hollow fiber module of filtration. For this purpose, based on the choice of membrane module configuration proposed in this study, and to strive for a rational optimization of the use of this device, the study relied on the use of CFD tools, supplemented by an experimental approach conducted under models conditions. The numerical simulations of fluid flow have shown a modification of the axial filtration velocity profile with packing density. Similarly, a numerical model of cake deposit was developed and show difference of cake growth along the fiber with packing density. Two experimental hollow fiber modules with two packing densities were tested with clean water and biological fluid, and showed good agreement with the numerical data. These results underline the variations of filtration velocity along the fiber that will allow some predictions on fouling deposit to be done
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Ghasemalizadeh, Farid [Verfasser], Philippe [Akademischer Betreuer] Bastiaens, and Leif [Gutachter] Dehmelt. "Recursive interaction between encapsulated dynamic microtubule asters and deformable membranes / Farid Ghasemalizadeh ; Gutachter: Leif Dehmelt ; Betreuer: Philippe Bastiaens." Dortmund : Universitätsbibliothek Dortmund, 2019. http://d-nb.info/1213975972/34.
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Wheeler, Sophia. "Physical properties of mixed membranes explored using atomistic and coarse grained molecular dynamic simulations with enhanced sampling techniques." Thesis, University of Southampton, 2018. https://eprints.soton.ac.uk/425867/.
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Studies of three different, but interlinked, aspects of membrane properties are presented here. First an analysis of both the lyotropic and thermotropic phase transitions of a phospholipid bilayer using the ELBA1.0 forcefield. This is believed to be the first time such transitions (including the rippled gel phase) have been observed using a coarse grained (CG) forcefield not specifically parameterised to do so. Further, analysis via enhanced sampling methods of the relative free energies of the phases is presented. These analyses confirm the enormous effects comparatively small changes to a forcefield can have on the aggregate behaviour of lipids modelled with it. Molecular dynamics studies on the bending rigidity of bilayers are also presented, including a comparison of 4 different computational methods for calculating the bending rigidity of bilayers. The system size dependency of such methods is compared, as well as their ability to reproduce trends in bending rigidity across lipid species already measured experimentally. The methods are compared across two different atomistic and one CG method for the first time and, despite quite different theoretical bases, are shown to produce surprisingly consistent results both with each other and with previously published experiment. Finally, two new parameterisations of cholesterol using the ELBA forcefield are explored. Their ability to induce the ordering and structure seen in atomistic simulations is measured and compared with another widely using coarse grained forcefield. ELBA's unique (amongst CG forcefields) direct compatibility with atomistic forcefields also allowed dual-resolution simulations of binary bilayers to be analysed. Results from such dual-resolution simulations are consistent with those resulting from atomistic simulation.
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Saad, Ahmad. "Les tannins du vins et les lipides de la bouche et du bol alimentaire : vers une modification des marqueurs du goût. Une approche moléculaire et sensorielle." Thesis, Bordeaux, 2017. http://www.theses.fr/2017BORD0879/document.
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Les tannins sont des polymères de polyphénols présents en quantité significative dans le vin rouge, et responsables de l’astringence et de l’amertume. L’astringence est une sensation de sècheresse et de rugosité en bouche résultant d’une forte interaction entre les tannins et les protéines de la salive impliquées dans la lubrification de la cavité buccale. L’amertume, quant à elle, est un goût stricto sensu résultant de l’interaction spécifique des tannins avec les récepteurs du goût situés dans les papilles linguales. Des études récentes ont montré que les tannins sont susceptibles d’interagir avec les lipides. Or les lipides sont présents lors de la dégustation d’un vin comme composants des membranes buccales ou des aliments gras. Cependant, le rôle des lipides dans les perceptions sensorielles d’un vin n’est pas bien connu d’un point de vue œnologique. L’objectif de cette thèse était d’étudier au niveau moléculaire les interactions tannin-lipide, pour mieux comprendre leur rôle dans les propriétés gustatives du vin. Le présent travail décrit l’effet de deux entités représentatives des tannins du vin : un monomère, la catéchine, et un dimère, la procyanidine B1, sur deux modèles lipidiques. Le premier modèle est un modèle membranaire représenté par des vésicules multilamellaires composées de POPC/Cholestérol (70/30), qui mime la composition lipidique des membranes buccales. Le deuxième modèle est une émulsion huile dans l’eau (H/E) stabilisée par le DMPC, qui mime les gouttelettes lipidiques présentes dans les aliments gras. L’organisation et la dynamique des lipides composant ces deux modèles ont été étudiées par la spectroscopie RMN (1H, 2H, 13C) en présence et en absence des deux entités de tannins. Leur localisation dans les membranes lipidiques a également été explorée, de même que leur affinité pour les lipides avec la détermination des constantes d’association tannin-lipide. Les résultats ont mis en évidence un effet fluidifiant des tannins à la fois sur le modèle de membranes buccales et sur le modèle de gouttelettes lipidiques. On a démontré que cet effet de désordre est lié à la nature chimique des tannins, ainsi qu’à leur position dans la membrane. De plus, les résultats sur l’affinité tannin-lipide sont en faveur d’une compétition avec les protéines salivaires. En outre, les résultats de biophysique se sont avérés conformes avec ceux d’une analyse sensorielle menée en parallèle qui a révélé que les aliments gras sont susceptibles de diminuer l’astringence du vin. Ces travaux montrent l’impact des composés phénoliques sur l’ordre membranaire et soulignent pour la première fois un rôle potentiel des lipides sur le goût du vin. D’une part, les interactions tannin-lipide, en perturbant l’environnement lipidique des récepteurs du goût enchâssés dans les membranes buccales, pourraient affecter la fonctionnalité du récepteur et son interaction avec les tannins, et donc l’amertume. D’autre part, une éventuelle compétition entre les interactions tannin-lipide et tannin-protéine de la salive pourrait diminuer l’astringence durant la dégustation d’un vin. Dans le domaine de l’œnologie, cette thèse vient étayer le ressenti des dégustateurs à savoir la modification du goût du vin due aux aliments et ouvre de nouvelles perspectives dans le cadre de l’association mets-vinsTannins are polyphenol polymers present in significant amounts in red wine responsible for astringency and bitterness. The former is a tactile perception involving dryness and roughness in the mouth due to the interaction between tannins and saliva proteins and the latter is a primary taste due to the interaction between tannins and taste receptors in taste buds. Tannins are now known to also interact with lipids. Although not present in wine, lipids are yet present during tasting in the oral membranes of tasters and in fatty foods when wine is consumed during a meal. However, although the influence of lipids is well known to wine tasters through food pairing, there is no scientific evidence to support this hedonic feeling. The aim of the thesis is to study tannin-lipid interactions at molecular level in order to better understand their implication in wine gustative properties. The present work describes the effect of the main representative grape tannin subunits, the catechin monomer and the B1 dimer, both on a model of oral membranes and food fat globules. They are represented by a dispersion of POPC/cholesterol multilamellar vesicles and a olive oil in water emulsion stabilized by DMPC as emulsifier, respectively. The organization and dynamics of the lipids composing these two models were investigated by solid-state NMR spectroscopy (1H, 2H, and 13C) in the absence and the presence of the two tannin subunits. The affinity of tannins for lipids was also explored by the determination of the thermodynamic association constant. The results pointed out a fluidizing effect of tannins both on the membrane model, as previously shown on a simpler membrane model, and on the emulsion lipid droplets. The disorder caused by tannins was shown to be related to their location in the lipid structure depending on the tannin chemical nature. Moreover, the strength of the interaction between tannins and membrane lipids was revealed to be in the same order of magnitude of that between tannins and saliva proteins. In addition, the biophysical results were in accordance with those of a sensory analysis led in parallel that revealed that fatty foods are prone to decrease wine astringency. These pioneering works shows the impact of phenolic compound on membrane order and highlight for the first time the potential role of the tannin-lipid interactions on wine taste. On the one hand, by disrupting the lipid environment of taste receptors embedded in oral membranes, tannin-lipid interactions could affect the receptor functionnality and therefore the interaction with tannin molecules, so bitterness. On the other hand, the existence of a possible competition between lipids and saliva proteins for interacting with tannins during tasting could reduce astringency
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Whitehead, L. "Computer simulation of biological membranes and membrane bound proteins." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297412.
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Zhang, Wenxiang. "Optimization of protein concentration from alfalfa juice by high shear rate dynamic filtration." Thesis, Compiègne, 2016. http://www.theses.fr/2016COMP2281/document.
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Les protéines extraites des feuilles de luzerne sont une source importante de protéines. La filtration membranaire, technologie de séparation respectueuse de l’environnement avec une productivité élevée et de faible coût a été utilisée pour séparer et concentrer les protéines des feuilles de luzerne à partir de leur jus. Cependant le phénomène du colmatage de la membrane qui réduit sérieusement le flux et la séparation des protéines est un facteur limitant important dans l'application de la filtration membranaire. Pour améliorer la récupération des protéines et amenuiser le phénomène du colmatage, la filtration membranaire associée à fort cisaillement a été utilisée pour la filtration du jus de luzerne. Toujours dans l’objectif d'optimiser le processus de la filtration, "le mode de la filtration" et "les paramètres de fonctionnement" ont été étudiés pour réduire le colmatage de la membrane et améliorer le rendement de la filtration. Puis, l’effluent du jus de luzerne a été filtré par des membranes dans des conditions de fort cisaillement afin de recycler les protéines. En outre, le mécanisme du colmatage a été étudié et a permis d’évaluer les stratégies de contrôle du colmatage. L'optimisation du procédé membranaire, via l’étude du "mode de filtration" et des "paramètres de fonctionnement" a été conduit dans le but d’améliorer la séparation et la concentration des protéines et de réduire le colmatage. Trois types de « mode de filtration » ont été testés : la filtration frontale sur le module de la cellule amicon (DA), la filtration tangentielle dynamique sur le module à disque rotatif (CRDM) et la filtration frontale sur le module à disque rotatif (DRDM)). Les « paramètres de fonctionnement » qui ont été étudiés sont les suivants : le type de membranes (ultrafiltration (UF) et microfiltration (MF)), la vitesse de rotation, la température et la pression transmembranaire (TMP). Le comportement du débit (évolution du flux du perméat au cours de la filtration), les performances de la séparation (taux de clarification et de concentration), l’efficacité du nettoyage de la membrane (récupération de la perméabilité membranaire) et la productivité lors des tests de recyclage et de concentration ont été étudiés dans le but de définir des stratégies dans le contrôle du colmatage. Puis, l’effluent de luzerne a été filtré par UF afin de séparer et purifier les protéines. Le mécanisme du phénomène du colmatage des membranes lors de la filtration du jus de luzerne a été étudié. Le processus du colmatage de la membrane a montré une tendance d’un colmatage multi-site progressif. Le modèle du colmatage multisite progressif selon la loi de Darcy (SMDM) a été proposé afin de mieux décrire et comprendre le processus du colmatage. Les effets de la composition du fluide d’alimentation, du choix de la membrane et des conditions hydraulique ont joué un rôle important dans le processus progressif du colmatage. De plus, les coefficients de résistance et de compressibilité dans les différentes étapes et sites ont été calculés afin d’expliquer le processus complexe du colmatage et d’évaluer l'efficacité des stratégies du contrôle du colmatage. Une série d'essais avec de longues durées de filtration a été réalisée pour étudier le déclin du flux et le colmatage de la membrane à diverses étapes du processus. Ces résultats présentent une utilité pour améliorer la récupération des protéines et contrôler le colmatage dans le processus de la filtration membranaire à fort cisaillement du jus de luzerne. Ces résultats sont aussi utiles pour la conception et la mise en place des technologies membranaires dans les processus industrielsAlfalfa leaf proteins extracted from plants are an important protein source. As an environmentally friendly separation technology with high productivity and low cost, membrane filtration was used to separate and concentrate leaf protein from alfalfa juice. However membrane fouling seriously reduces flux and protein separation and is an important limitation in the application of membrane filtration. To improve protein recovery and fouling control, dynamic shear-enhanced membrane filtration with high shear rate on membrane surface and excellent anti-fouling capacity was used for alfalfa juice filtration in this work. In order to optimize filtration process, filtration mode and operation parameters were investigated to reduce membrane fouling and improve separation performance. Then, alfalfa wastewater was also treated by dynamic shear-enhanced membrane filtration to recycle proteins. Furthermore, the fouling mechanism was studied and served as a valuable evaluation for fouling strategies. In this study, process optimization including “Filtration mode” and “Operation parameters” was studied to improve protein recovery and fouling control. In “Filtration mode”, three types of filtration modules (dead end filtration using laboratory Amicon cell (DA), dynamic cross filtration using rotating disk module (CRDM) and dead end filtration using rotating disk module (DRDM)) were used to investigate the filtration performance. As for “Operation parameters”, the operation parameters including membranes (ultrafiltration (UF) and microfiltration (MF)), rotating speed, temperature and transmembrane pressure (TMP) were studied to optimize the filtration process. Flux behavior (permeate flux and flux decline), separation performance (clarification and concentration capacity), membrane cleaning efficiency (permeability recovery) and productivity in full recycling tests and concentration tests were utilized to evaluate the various operation strategies. In addition, alfalfa wastewater was treated by UF membrane, while waste proteins were recycled. Fouling mechanism for alfalfa juice filtration was investigated. The fouling process showed significantly stepwise multisite patterns. Based on Darcy’s law, the stepwise multisite Darcy’s law model (SMDM) was proposed to better describe and understand the fouling process. The effects of feed composition, membrane and hydraulic conditions played an important role in stepwise fouling process. Moreover, the resistance coefficient and compressibility for different steps and sites were calculated to explain the complex fouling process and estimate the efficiency of flux decline control strategies. Besides, a series of long tests were utilized to study flux decline and membrane fouling at various fouling step process. These results can be used to understand the protein recovery and fouling control during shear-enhanced membrane filtration process of alfalfa juice. They have important implications for process design of membrane technology in industrial scale
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De, Vecchis Dario. "Gaining insights into mitochondrial membrane fusion through a structural and dynamic atomistic model of the mitofusin Fzo1p." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCC001.
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Les mitochondries sont des organites dynamiques dont la morphologie dépend de l’équilibre fusion/fission de leurs membranes. Ce processus essentiel à la survie cellulaire est nommé dynamique mitochondriale et sa dérégulation est associée à des troubles neurologiques. Cependant les mécanismes précis régissant la dynamique mitochondriale ne sont pas élucidés. Cette thèse porte sur la protéine Fzo1p, une grande GTPase de la superfamille des Dynamin-related-Protein. C’est un élément clé impliqué dans la fusion mitochondriale de la membrane externe de la levure. Sa structure et sa dynamique ont été étudiées par modélisation et simulations de dynamiques moléculaires tout-atome dans une bicouche lipidique solvatée. Le modèle structural obtenu tient compte de données expérimentales, de template structuraux, et de modèles ab initio du domaine transmembranaire de Fzo1p. Ce modèle a été validé expérimentalement par mutagenèse dirigée. Des permutations de charges ont confirmé des ponts salins à longue distance prédits dans le modèle. En outre, des mutations ont montré que les domaines coiled-coil de Fzo1p, contrairement à sa partie N-terminale, sont indispensables à sa fonction. L’ensemble des résultats expérimentaux et in silico met en évidence l’implication des domaines charnières dans le changement conformationnel de Fzo1p, ainsi que des résidus critiques affectant sa stabilité. Les précisions atomiques obtenues sur l’interaction de Fzo1p avec le GDP permet de formuler des hypothèses sur le mécanisme moléculaire de la catalyse du GTP pour la fusion membranaire; voire à la compréhension de la dynamique mitochondrialeMitochondria are dynamic organelles whose morphology is determined by fusion and fission of their membranes. This essential process is known as mitochondrial dynamics. Defects in mitochondrial dynamics are associated with neurological disorders making the investigation of physiological relevance. However, the precise sequence of events that lead mitochondrial dynamics are still not well characterised. Fzo1p, a large GTPase of the Dynamin-Related Proteins superfamily, is a key component in mitochondrial outer membrane fusion in yeast. During this PhD project I built a model of the protein Fzo1p. The structure and dynamics of the model was investigated through molecular modelling and all-atom molecular dynamics simulation in a fully hydrated lipid bilayer environment. The Fzo1p structural model integrates information from several template structures, experimental knowledge, as well as ab initio models of the transmembrane segments. The model is validated experimentally through directed mutagenesis, for instance charge-swap mutations confirm predicted long-distance salt bridges. A series of mutants indicate that coiled-coil domains are required for protein function at variance with its N-terminal region. Overall, the experimental and in silico approaches pinpoint the hinge domains involved in the putative conformational change and identifies critical residues affecting protein stability. Finally, key Fzo1p-GDP interactions provide insights about the molecular mechanism of membrane fusion catalysis. The model provides insight on atomic level and proposes a structure that will be instructional to understanding mitochondrial membrane fusion
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Sadler, Emma Elizabeth. "Single-molecule fluorescence studies of KirBac1.1." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:214fcd74-7384-4ade-ac17-7cac5c44a05c.
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Inwardly rectifying potassium (Kir) channels are essential for controlling the excitability of eukaryotic cells, forming a key part of the inter-cellular signalling system in multi-cellular organisms. However, as prokaryotic (KirBac) channels are less technically challenging to study in vitro and have been shown to be directly homologous to eukaryotic channels, they are often studied in lieu of their mammalian counterparts. A vital feature of Kir and KirBac channels is their mechanism for opening and closing, or their gating: this study predominantly features observations of open and/or closed channel populations. A well-characterised member of the KirBac family, KirBac1.1, has been successfully expressed, purified into detergent micelles, and doubly labelled with fluorescent maleimide dyes in order to enable observation of confocal-in-solution Förster Resonance Energy Transfer (FRET) at the single molecule level. Results demonstrate single-molecule FRET signals from KirBac1.1 and therefore represent the first single-molecule FRET observations from a KirBac channel. Perturbation of the open-closed dynamic equilibrium was performed via activatory point mutations, changes in pH, and ligand binding. A protocol for reconstitution into nanodiscs was optimised in order to more closely approximate native conditions, and the single-molecule FRET observations repeated. This thesis presents a comparison between measurements made using the detergent solubilisation system and those made using nanodiscs.
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Dietrich, Undine [Verfasser], Josef Alfons [Akademischer Betreuer] Käs, Josef Alfons [Gutachter] Käs, and Helmuth [Gutachter] Möhwald. "Structural and dynamic studies of MARCKS interaction with PIP(2) containing lipid membranes / Undine Dietrich ; Gutachter: Josef Alfons Käs, Helmuth Möhwald ; Betreuer: Josef Alfons Käs." Leipzig : Universitätsbibliothek Leipzig, 2011. http://d-nb.info/1237895707/34.
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Nigam, Poonam. "Interaction of water-soluble surfactants with self-assembled lipid monolayers at the vapor-liquid interface equilibrium and dynamic phenomena /." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1157987838.
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Duncan, Anna Louise. "Coarse-grained molecular dynamics simulations of mitochondrial membrane proteins." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648455.
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Berrod, Quentin. "Relation structure - transport dans des membranes et matériaux modèles pour pile à combustible." Phd thesis, Université de Grenoble, 2013. http://tel.archives-ouvertes.fr/tel-00981913.
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L'optimisation des performances d'une pile à combustible (PEMFC) requiert la compréhension microscopique des mécanismes de transport de l'eau et du proton confinés au sein de la membrane électrolyte polymère. La membrane est un matériau nanostructuré chargé, caractérisé par une dynamique de l'eau et du proton complexe et multi-échelle étroitement corrélée à la morphologie confinante. Nous nous sommes intéressés à la relation structure - transport dans i) L'Aquivion, un ionomère perfluorosulfonique récent présentant de bonnes performances en pile, ii) des systèmes " modèles " auto-assemblés de tensioactifs perfluorés formant des phases lamellaires et hexagonales et iii) une nouvelle membrane hybride préparée par dopage en tensioactif. La nano-structuration des différents systèmes a été étudiée par diffusion de rayonnement (X et neutrons), pour caractériser l'évolution de la structure (géométrie de la matrice hôte, taille de confinement) avec l'hydratation. Ensuite, nous avons sondé la dynamique de l'eau à l'échelle moléculaire (de la picoseconde à la nanoseconde) par diffusion quasi-élastique des neutrons (QENS) et à l'échelle micrométrique par RMN à gradients de champs pulsés. La comparaison membranes commerciales / systèmes modèles permet de discuter l'impact de la connectivité, du confinement et de la géométrie sur le transport ionique. Enfin, des membranes hybrides à fort potentiel ont été obtenues par dopage du Nafion et de l'Aquivion avec des tensioactifs. Ces nouveaux matériaux ouvrent une voie prometteuse pour la préparation de membranes polymères fortement anisotropes avec des chemins de conduction préférentiellement orientés.
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Costello, Michael John School of Chemical Engineering & Industrial Chemistry UNSW. "SHELL-SIDE FLUID DYNAMICS AND MASS TRANSFER THROUGH HOLLOW FIBRE MEMBRANE MODULES." Awarded by:University of New South Wales. School of Chemical Engineering and Industrial Chemistry, 1995. http://handle.unsw.edu.au/1959.4/17042.
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There is a considerable volume of work available in literature which suggests that the performance of axial-flow hollow fibre membrane modules is limited by poorly distributed flow through the shell-side. This study was commissioned to examine the distribution of shell-side flow and its effect on mass transfer and to compare the performance measured by the axial-flow configuration to that obtained by a commonly used alternative known as the helically-wound module design. Laminar flow and mass transfer models have been developed to examine performance through axial-flow hollow fibre modules. These models also consider deviations from laminar flow in the form of turbulence and hydrodynamically undeveloped flow. Modelling analysis on four fibre bundle cross-sections quantify the extent to which channelling limits flow and mass transfer performance. Experimental flow and mass transfer work with locally fabricated hollow fibre modules demonstrated some inconsistencies with axial laminar flow modelling. Pressure drop and mass transfer results exceeded predictions from modelling. This thesis has hypothesised that fibres in axial-flow hollow fibre modules are not aligned as straight and parallel rods (as assumed in modelling) but interweave. Fibre interweaving results in flows between ducts. Such flows create mixing between ducts which results in more intimate contact between the flow and membrane surface, the consequence being higher pressure drop and higher mass transfer. The implication from this work was that axial flow and mass transfer modelling was limited in its use for characterisation of shell-side performance. The experience with helically-wound hollow fibre membrane modules (also fabricated locally) was that, by deliberately inducing flow between ducts, it was possible to considerably improve mass transfer performance. It was found that, whilst helically-wound modules could not be packed as tightly as axial-flow modules and required more sophisticated fabrication techniques, the benefit in their use arose from a substantial improvement in the level of shell-side mass transfer.
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Trochmann, Jose Luiz Lino. "Simulação atomistica como ferramenta para investigação dos mecanismos de difusão : coeficientes de autodifusão de gases simples em matriz polimerica." [s.n.], 2006. http://repositorio.unicamp.br/jspui/handle/REPOSIP/266175.
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Orientador: Sergio Persio RavagnaniTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica
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Resumo: Neste trabalho de tese foi realizado um estudo do potencial de predição de propriedades de transporte em matrizes poliméricas de poli - imidas, utilizando a simulação dinâmica molecular de gases simples como Oxigênio, Nitrogênio e Dióxido de Carbono. A propriedade de transporte de interesse prático, a permeabilidade de uma membrana polimérica a um dado penetrante, envolve a determinação de propriedades de ordem cinética e termodinâmica, respectivamente a determinação do coeficiente de difusão e da solubilidade deste penetrante na matriz polimérica. Atenção especial foi conferida à propriedade cinética, pela predição do coeficiente de autodifusão dos penetrantes. Num procedimento experimental clássico é de vital importância para significância das conclusões derivadas dos experimentos, o uso de amostras de membranas poliméricas adequadamente preparadas quanto à composição química, estrutura física e morfologia. Analogamente, quando se utiliza a simulação molecular para a predição de propriedades, tais como o coeficiente de autodifusão, também é de fundamental relevância para os resultados obtidos, a qualidade dos modelos moleculares das matrizes poliméricas, que serão usados como base. Assim para a preparação de modelos moleculares com o adequado empacotamento, um procedimento para a obtenção de modelos bem equilibrados foi desenvolvido neste trabalho. Os modelos moleculares desenvolvidos foram usados para a obtenção dos valores de massa específica em função da temperatura, e comparados aos valores experimentais disponíveis e quando necessário a, valores preditos por meio da expressão de massa específica em função da temperatura, acima e abaixo da temperatura de transição. A capacidade do modelo molecular desenvolvido em predizer a massa especifica e temperatura de transição vítrea foi usada como critério para a validação da adequação do empacotamento proposto para o referido modelo molecular da matriz polimérica. Os modelos validados de empacotamento, células amorfas, foram utilizados para o cálculo do coeficiente de autodifusão dos gases acima mencionados, através do da simulação dinâmica molecular. A comparação dos coeficientes de autodifusão obtidos das poli-imidas aromáticas e éster imidas, BAAF, 6FDA-ODA, PMDA-ODA e BA-20DA, para os gases O2, N2 e CO2, com os dados experimentais, permitiu concluir a adequação das células amorfas e do esquema de simulação dinâmica molecular para a predição do coeficiente de autodifusão.. A versão preditiva de Vrentas e Duda, baseada na teoria do volume livre, foi utilizada para a predição dos coeficientes de autodifusão da água e do etanol para as poli-imidas acima. , Estes valores, quando comparados com os valores obtidos através da simulação dinâmica molecular mostram a validade de ambas as teorias para a predição da cinética de difusão de penetrantes em matrizes poliméricas complexas
Abstract: In this thesis a study of the predictive potential of the molecular dynamic simulation was performed for transport properties of light gases in polyimide matrix. From de practical point of view permeability is the property of most interest, and involves kinetics as well as thermodynamics properties, diffusion coefficient and solubility of the penetrants molecule in the bulk polymeric matrix, this work will be focus in the former. As important as is in as experimental work, a well prepared polymeric membrane is essential for the significance of the draw conclusions. Therefore a special attention was take in the preparation of the bulk molecular polymeric model, the so called amorphous cell, in order to obtain well-equilibrated molecular packing models for the polyimide matrixes. The amorphous cells were prepared throughout thermodynamic transforms, using one or more of the statistical ensembles and cell specific volume obtained as a function of temperature, this data was compared against the experimental data available, and when necessary to data obtained via predictive methods. The molecular packing model ability to predict the glass transition temperature was used as criteria to validate de amorphous cell, to be used in the molecular dynamic' simulations allow the matrix to be locally flexible and coupled to the classic molecular dynamics simulation. The resulting self diffusion coefficients for the polyimide, BAAF, 6FDA-ODA, PMDAODA and BA-20DA for the gases O2, N2 e CO2 were compared to the experimental data. The lack of quality experimental diffusion data available for polyimide membranes for larger penetrants as water and ethanol, showed up as a good opportunity to assess the predictive capability of the molecular dynamic simulation for self diffusion coefficients, considering the relevant technological relevance of polyimide membranes for pervaporation process. The data of self diffusion coefficient produced by the predictive version of free-volume theory after Vrentas and Duda, was compared with the data produced via coupled molecular dynamic simulation for the water and ethanol penetrants, showing the relevance of both theories for the prediction of penetrants kinetic in complex polymeric matrixes
Doutorado
Ciencia e Tecnologia de Materiais
Doutor em Engenharia Química
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Luna, Escalante Juan Camilo. "Spatio-temporal dynamics of intercellular Notch signaling: a modeling approach." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/400610.
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Intercellular signalling is a mechanism by which cells communicate and mediate coordinated responses. In this Thesis we perform theoretical and computational analyses to evaluate spatio-temporal organizations that can arise in developing embryos through juxtacrine signalling mediated by Notch receptor. Juxtacrine signalling is a type of intercellular communication in which adjacent cells mutually interact through membrane-attached proteins (receptors and ligands). In the case of Notch signalling, the ligands are regulated by the signalling, establishing a feedback loop on the activation of the signal between adjacent cells.
Our study focused on the following open questions:
1. What coordinated responses arise when Notch signalling is activated by two (or more) co-expressing ligands?
2. What is the effect on the response mediated by Notch signalling when
considering a gene involved in cell differentiation that promotes it on transcription, but in turn is repressed by the signal?
3. Which processes can modulate the signalling efficiency of a ligand?
These questions encompass aspects occurring at different levels, ranging from the type of response that arises in a tissue (salt-and-pepper patterning, homogeneous states or propagation of a cell fate in an expansive wave), the signalling state of cells (sending, receiver, among others), up to the dynamics of the intracellular processing of Notch. We used a modelling and computational approach for their study and compared, when possible, with previously reported phenotypes in developing embryos.La vía de señalización de Notch es un mecanismo de comunicación inter-celular yuxtacrina. La señal de Notch se activa tras la unión del ligando en una célula con el receptor en otro célula adyacente. La vía de Notch está ampliamente asociada a respuestas de coordinación espacio-temporal que ocurren durante el desarrollo de Metazoos, como es la formación de los patrones salt-and-pepper. Cómo Notch puede mediar este tipo de respuestas es una pregunta de gran interés tanto en física de sistemas alejados del equilibrio como en biología del desarrollo. Numerosos trabajos experimentales y teóricos han servido para entender el funcionamiento de la vía de Notch y su papel en la formación de respuestas complejas. Sin embargo, quedan ciertas preguntas sin responder aún. En esta Tesis abordamos algunas de estas cuestiones, utilizando una aproximación teórica y computacional y comparando nuestros resultados cuando es posible con fenotipos publicados con anterioridad. Las preguntas abordadas son: 1. Es bien sabido que la señal de Notch puede ser activada por distintos tipos de ligando, los cuales pueden expresarse simultáneamente durante el desarrollo. Por tanto nos preguntamos, ¿Qué respuestas de coordinación espacio-temporal surgen cuando la señal de Notch es activada por varios tipos de ligando? Nuestros resultados evalúan la relevancia de compartir y competir por recursos para la señalización y de diferencias de la eficiencia de señalización entre ligandos en la aparcición de organizaciones espacio- temporales (patrones periódicos de dos tipos celulares, por ejemplo) y en los estados de señalización de las células. 2. Es conocido que la inhibición lateral mutua entre células adyacentes mediada por Notch es un mecanismo suficiente para generar patrones periódicos de dos tipos celulares. Además, la vía de Notch implica numerosos pasos, entre ellos, retroalimentaciones positivas dentro de la propia célula de los genes que regulan la diferenciación. ¿Qué efecto tiene esta retroalimentación en la respuesta mediada por Notch? Nuestros resultados muestran que dicha auto-activación hace robusta la diferenciación celular. 3. Diferentes ligandos pueden activar distintos niveles de la señal de Notch. Estas diferencias pueden estar mediadas por modificaciones post-transduccionales del receptor Notch. Nos preguntamos ¿Qué procesos durante la formación de la señal pueden modular la eficiencia de señalización de los ligandos? Nuestros resultados muestran cómo la eficiencia de señalización de un ligando depende de la dinámica de procesamiento y degradación del complejo receptor-ligando.
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Woo, Sahng Hyuck. "Membranes composites acide perfluorosulfonique (PFSA)/argile pour un fonctionnement à faible humidité relative et haute température des piles à combustible à membrane échangeuse de protons (PEMFC)." Thesis, Paris Sciences et Lettres (ComUE), 2019. http://www.theses.fr/2019PSLEM033.
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Cette thèse introduit de nouvelles membranes électrolytiques pouvant fonctionner à faible humidité relative (inférieure à 50%) et à une température intermédiaire, c'est-à-dire 90°C voire au-delà. Plus spécifiquement, la thèse tire profit de l'hygroscopicité de la morphologie d’argiles naturelles, lasépiolite microfibreuse et l’halloysite tubulaire . Ces nanoargiles ont été intégrées à des suspensions de Nafion® ou Aquivion pour préparer des membranes composites. Elles ont été fonctionnalisées et prétraitées pour les rendre conductrices protoniques et améliorer leur compatibilité avec les matrices perfluorosulfoniques utilisés. Ces argiles ont d’abord été caractérisées avant leur incorporation dans la matrice polymère : ATR-FTIR (spectroscopie infrarouge à transformée de Fourier totale atténuée), Py-GC/MS (spectrométrie de masse par chromatographie en phase gazeuse à pyrolyse) et ATG (analyse thermogravimétrique). Les propriétés des nanoargiles prétraitées ont enfin été caractérisées par XRD (diffraction des rayons X) et EDS. Les membranes composites préparées ont ensuite été caractérisées pour la conductivité protonique, l'absorption d'eau, le gonflement, la résistance thermomécanique et la stabilité chimique. L'état de dispersion des argiles à l'intérieur de la phase de polymère a été observé par SEM/EDS (microscopie électronique à balayage à émission de champ / spectroscopie à rayons X à dispersion d'énergie). La stabilité chimique vis-à-vis de l'attaque radicale contre les membranes composites a été étudiée par mesure de la formation d’ions fluorure (F-). La conductivité protonique des membranes composites a également été calculée à partir des résistances mesurées dans dans une large gamme d'humidités relatives et de températures. Des mesures thermomécaniques par analyse mécanique dynamique ont montré que la morphologie allongée particulière des argiles choisies participe à l'amélioration des propriétés mécaniques des membranes composites tout en réduisant le taux de gonflement. Les performances en assemblage membrane électrodes ont été évaluées pour mettre en évidence l’avantage de la présence de ces nanoargiles dans les membranes composites en ce qui concerne l’humidité relative du gaz d’alimentation, la température de fonctionnement de la cellule et la perméation à l’hydrogène. Des résumés détaillés comprenant les principaux résultats ont été fournis au début de chaque chapitreThis thesis introduces novel electrolyte membranes which can be operated at low relative humidity (below 50%) and intermediate temperature, i.e., 90℃. More specifically, the thesis takes benefit from hygroscopicity of microfibrous SEP (sepiolite) and tubular HNT (halloysite). Changes in Nafion membrane properties with blending time were studied. Moreover, these nanoclays are functionalized and pretreated to make them proton conductive and to improve their compatibility with short-side-chain PFSA (perfluorosulfonic acid) composite membranes based on Aquivion. To begin with, functionalized and pretreated clay nanoparticles are characterized prior to incorporation in polymer matrix: ATR-FTIR (attenuated total reflection-fourier transform infrared spectroscopy), Py-GC/MS (pyrolysis gas chromatography mass spectrometry), and TGA (thermogravimetric analysis). Composites membranes have them been prepared and characterized for proton conductivity, water uptake, swelling, thermo-mechanical strength and chemical stability. The dispersion state of SEP and HNT inside polymer phase was observed using SEM/EDS (field emission scanning electron microscopy/Energy dispersive X-ray spectroscopy). The properties of pretreated nanoclays are characterized using XRD (X-ray diffraction) and EDS. Chemical stability regarding radical attack against composite membranes is clarified using Ion meter through fluoride ion (F-) analysis. Proton conductivity of composite membranes is also measured under condition of different relative humidity and temperature. Following this, it is demonstrated by DMA (dynamic mechanical analysis) results that the particular elongated morphology of SEPs and HNTs participates to improving mechanical property of the composite membranes with decreased swelling ratio. MEAs (membrane electrode assembly) performance are evaluated to understand the advantage of the presence of nanoclays in the composite membranes regarding the relative humidity of the feeding gas, the operating temperature of the cell, and the hydrogen crossover. Detailed abstracts including main results were provided at the beginning of each chapter
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Tarazaga, Pablo Alberto. "Dynamics and Control of a Pressurized Optical Membranes." Diss., Virginia Tech, 2009. http://hdl.handle.net/10919/28727.
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Optical membranes are currently pursued for their ability to replace the conventional mirrors that are used to correct wave front aberration and space-based telescopes. Among some of the many benefits of using optical membranes, is their ability to considerably reduce the weight of the structure. As a secondary effect, the cost of transportation, which is of great interest in space applications, is reduced as well. Given the low density of these thin-film membranes, the lower end dynamics play a greater significant role than their rigid plate-like counterparts in achieving functional mirrors. Space-based mirrors are subjected to a series of disturbances. Among those encountered are thermal radiation, debris impact, and slewing maneuvers. Thus, dynamic control is essential for the adequate performance of thin-film membrane mirrors.
With this in mind, the work described herein aims to improve the performance of optical membranes with an innovative, acoustical control approach to suppress vibration of optical membranes backed by an air cavity. This is achieved by using a centralized acoustic source in the cavity as the method of actuation. The acoustic actuation is of great interest since it does not mass load the membrane in the conventional way, as most methods of actuation would.
To achieve this end goal, two structural-acoustic coupled models are developed to describe the dynamics of a pressurized optical membrane system. This is done through an impedance based modeling approach where the subsystems are modeled individually, and then coupled at the interface. The control of the membrane is implemented using a positive position feedback approach. The theory is also extended to positive velocity and positive acceleration feedback.
Three experiments are carried out to validate the models previously mentioned. Successful implementation of a control experiment is also accomplished leading to considerable attenuations in the coupled membraneâ s dynamics.Ph. D.
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Kiselev, Vladimir. "Computational study of electrostatic contribution to membrane dynamics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5751.
Full textAbstract:
Electrostatics plays a crucial role in the membrane biology. Negatively charged lipids (such as PS, PA and PIP2) are subject to redistribution under the action of electrostatic forces during various signalling events. Membrane recruitment of multiple signalling proteins (such as MARCKS or Src kinase) is often maintained by positively charged polybasic domains (PD). Even though adsorption of these proteins to the cellular membrane has been extensively investigated, very little is known about how electrostatic interactions contribute to their membrane lateral dynamics. This thesis presents an investigation of the contribution of electrostatic interactions to the membrane lateral dynamics by means of novel computational tools. First, I developed a dynamic Monte-Carlo automaton that faithfully simulates lateral diffusion of the adsorbed positively charged PD of a peripheral membrane protein, as well as the dynamics of mono- (PS, PA) and polyvalent (PIP2) anionic lipids within the bilayer. This model allowed to investigate the major characteristics of protein-membrane diffusion on the uniform membrane. In agreement with earlier results, the simulations revealed the following microscopic phenomena: 1) Electrostatic lipid demixing in the vicinity of the PD; 2) PD interacts with PIP2 stronger than with monovalent lipids. On the spatially heterogeneous membrane the automaton predicted a directional drift of the PD, which was validated by a simple mean-field analytical model. The predicted phenomenon could potentially play a major role in membrane domain formation. To test this hypothesis and to investigate the membrane dynamics on larger scales I developed a continuous model, which was based on the results of the automaton simulations. The results of the continuous model and the Monte-Carlo simulations were shown to be in quantitative agreement. The continuous model allows one to simulate the electrostatic membrane dynamics on micrometer scales and can be used to describe various biologically important processes, such as endocytic cup initiation.
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Witkowski, Thomas, Rainer Backofen, and Axel Voigt. "The influence of membrane bound proteins on phase separation and coarsening in cell membranes." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-139226.
Full textAbstract:
A theoretical explanation of the existence of lipid rafts in cell membranes remains a topic of lively debate. Large, micrometer sized rafts are readily observed in artificial membranes and can be explained using thermodynamic models for phase separation and coarsening. In live cells such domains are not observed and various models are proposed to describe why the systems do not coarsen. We review these attempts critically and show within a phase field approach that membrane bound proteins have the potential to explain the different behaviour observed in vitro and in vivo. Large scale simulations are performed to compute scaling laws and size distribution functions under the influence of membrane bound proteins and to observe a significant slow down of the domain coarsening at longer times and a breakdown of the self-similarity of the size-distribution functionDieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich
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Zheng, Yu Zi. "Dynamic composition of membrane microdomains." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/42789.
Full textAbstract:
Lipid rafts are cholesterol enriched membrane microdomains involved in many cellular functions. Caveolae are a sub-type of lipid rafts that are smooth invaginations of the plasma membrane (PM) whose formation requires caveolin-1 (Cav1). Here, we determined the lipid rafts and caveolae proteome from various cells in an unbiased manner and examined the dynamic raft proteome change during Salmonella infection using quantitative proteomics. In chapter 2, we approach the status of mitochondrial proteins in detergent-resistant membrane (DRM) preparations by employing Stable Isotope Labeling by Amino acids in Cell culture (SILAC) to evaluate the composition of differentially purified subcellular fractions. Our data demonstrate that mitochondrial proteins that were previously identified as raft components are partially co-purifying contaminants of raft preparations. In tumor cells deficient for Golgi β-1,6N-acetylglucosaminyltransferase V (Mgat5), reduced Cav1 expression is associated not with caveolae but with oligomerized Cav1 domains, or scaffolds. These cell lines displaying differing Cav1/caveolae phenotypes are effective tools for probing the composition of caveolae. Using SILAC in chapter 3, we are able to quantitatively distinguish the composition of caveolae from the background of DRM proteins and show that the presence of caveolae enriches protein composition of DRM, including the recruitment of multiple heterotrimeric G-protein subunits. Furthermore in chapter 4, we explored the dynamic change of membrane protein composition according to an external signal. Salmonella are Gram-negative intracellular bacteria believed to attack lipid rafts as the site of entry. We applied SILAC examined the change of host raft proteome at a couple of time points during Salmonella infection. Dozens of proteins have shown to be highly regulated, one of them – Cav1 is shown to be required by Salmonella entrance. We also developed a high-content screening assay that is able to estimate the number of bacteria entered or survived inside the host for future functional studies of the novel proteins identified. This research gives us a better understanding of the raft proteome and how rafts are localized, as well as it can be changed. The Salmonella infection work leads to a global raft proteome dynamic analysis and identifies several proteins that may be novel bacterial host targets.
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Roengpithya, Chayaporn. "Membrane enhanced dynamic kinetic resolution." Thesis, Imperial College London, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438187.
Full text
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Parrett, Mark. "Membrane enhanced dynamic kinetic resolution." Thesis, University of Warwick, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441625.
Full text
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Witkowski, Thomas, Rainer Backofen, and Axel Voigt. "The influence of membrane bound proteins on phase separation and coarsening in cell membranes." Royal Society of Chemistry, 2012. https://tud.qucosa.de/id/qucosa%3A27814.
Full textAbstract:
A theoretical explanation of the existence of lipid rafts in cell membranes remains a topic of lively debate. Large, micrometer sized rafts are readily observed in artificial membranes and can be explained using thermodynamic models for phase separation and coarsening. In live cells such domains are not observed and various models are proposed to describe why the systems do not coarsen. We review these attempts critically and show within a phase field approach that membrane bound proteins have the potential to explain the different behaviour observed in vitro and in vivo. Large scale simulations are performed to compute scaling laws and size distribution functions under the influence of membrane bound proteins and to observe a significant slow down of the domain coarsening at longer times and a breakdown of the self-similarity of the size-distribution function.Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.
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Bertot, Laëtitia. "Le rôle des protéines courbant les membranes dans l’endocytose indépendante de la clathrine suivie par le récepteur de l’interleukine 2." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS570/document.
Full textAbstract:
L’endocytose permet l’internalisation d’éléments présents dans le milieu extracellulaire tels que les nutriments. Ce processus prend place dans la membrane plasmique. Les courbures de la membrane jouent un rôle essentiel dans l’endocytose pour générer une invagination initiale, un puits, puis une vésicule qui se sépare ensuite de la membrane plasmique pour fusionner avec les compartiments intracellulaires. Il existe plusieurs voies d’endocytose qui peuvent être classées selon des critères tels que la taille des vésicules produites, la médiation par un récepteur ou la présence d’un manteau recouvrant les vésicules. La voie d’endocytose la mieux caractérisée est celle dépendante de la clathrine. Mon laboratoire d’accueil travaille sur l’entrée du récepteur de l’interleukine 2 (IL-2R). Ce récepteur peut entrer de façon constitutive ou induite en présence de son ligand l’IL-2. Les deux voies sont indépendantes de la clathrine. Lors de mon arrivée dans le laboratoire, ces voies étaient encore peu caractérisées, notamment les facteurs induisant les courbures membranaires restaient à identifier. Ces facteurs doivent être particulièrement impliqués car les vésicules contenant l’IL-2R sont dépourvues de manteaux. Un crible par interférence à ARN, réalisé avant mon arrivée avait permis de proposer des protéines candidates pouvant courber les membranes. La première partie de ma thèse a consisté à confirmer l’importance de certaines protéines issues de ce crible puis à étudier leurs rôles dans la voie constitutive de l’IL-2R. Parmi ces protéines confirmées, deux familles de facteurs étaient particulièrement intéressantes pour leur capacité à courber les membranes, les phospholipases D et les endophilines. Ces dernières ont permis d’identifier une nouvelle voie d’entrée nommée « Fast Endophilin Mediated Endocytosis » FEME dans laquelle l’endophiline joue un rôle essentiel et qui est empruntée par de nombreux récepteurs transmettant le signal. La voie FEME partage plusieurs facteurs communs avec la voie d’endocytose induite de l’IL-2R. Pour finir, mes travaux de thèse ont porté sur l’orchestration de l’endophiline et de la dynamine dans la voie d’endocytose constitutive de l’IL-2R. Ces deux facteurs sont impliqués en fin d’endocytose, pour scinder les vésicules de la membrane plasmique. Cependant, ces deux protéines n’ont pas la même orchestration. Nos travaux montrent une action distincte de l’endophiline et de la dynamine dans les voies d’endocytose dépendante et indépendante de la clathrineEndocytosis allows the uptake of elements from the extracellular fluid such as nutriments. This process takes place at the plasma membrane. The membrane curvatures play an important role in endocytosis for the production of initial invagination to form a pit that will be then separate from the plasma membrane and will go to the intracellular compartments. Several routes of endocytosis exist and can be classified depending on vesicles size formed, receptor mediated endocytosis or coat on vesicles. The well-known characterized endocytosis pathway is the clathrin mediated one. My lab is working on interleukin 2 receptor (IL-2R) entry. This receptor can enter either constitutively or upon induction by the ligand IL-2. Both uptake pathways are independent of clathrin. When I arrived in the lab, those pathways were still under characterization, in particular the factors inducing the membrane curvature. Their role should be important since IL-2R containing vesicles are coated free. A small interfering RNA screen performed before my phD, allowed to identify new candidates. The first part of my thesis was to verify the involvement of some of them in the IL-2R constitutive pathway and then to study their role in this pathway. Among them, 2 families of proteins were particularly interesting as they can curve membranes, phospholipases D and endophilins. The endophilin allowed the discovery of a new route called “Fast Endophilin Mediated Endocytosis” (FEME) in which it plays an essential role and which is used by numerous receptors that transmit signal. The FEME pathway shares several factors that are common with the IL-2 induced endocytosis pathway. Then, I conducted a work on the orchestration of endophilin and dynamin during the constitutive IL-2R endocytosis. Both factors are recruited at the end of the mechanism, to separate the vesicles from the plasma membrane. However, both proteins do not have the same orchestration. Our works show a distinct action of endophilin and dynamin in clathrin dependent and independent endocytosis
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Gudejko, Heather F. M. "Membrane Dynamics During Cytokinesis." Thesis, Boston College, 2013. http://hdl.handle.net/2345/3781.
Full textAbstract:
Thesis advisor: David R. BurgessCytokinesis is the final step in cell division, culminating in the formation of two daughter cells from a single mother cell. Previous studies from our lab have shown that lipid rafts are dynamic during cytokinesis in sea urchin embryos, migrating into the ingressing cleavage furrow then moving back outwards towards the poles prior to abscission. Here, I quantitated the mobility of GM1, a ganglioside enriched in lipid rafts, using cholera toxin subunit B (CTB). Despite previous observations of raft movement during cell division, I have found lipid rafts to be immobile throughout the cell cycle. Lipid raft stability is dependent on the activity of myosin light chain kinase (MLCK), most likely due to the dramatic reorganization of actin filaments upon MLCK inhibition. While further investigating the immobility of lipid rafts during cytokinesis using confocal microscopy, I have found that new membrane is added to the cell poles during anaphase, causing the plasma membrane to expand coincident with the constriction of the contractile ring. This membrane addition is dependent on actin and astral microtubules and occurs significantly earlier during mitosis than membrane addition at the furrow. The membrane that is added at the polar regions is compositionally distinct from the original cell membrane in that it is devoid of GM1, a component of lipid rafts. I also found that Rab11 vesicles are trafficked to the polar plasma membrane during the time of this new membrane event, suggesting that the growth of the plasma membrane at the cell poles during cell division is not due to stretching as previously thought, but due to the addition of new membrane through exocytosis
Thesis (PhD) — Boston College, 2013
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Morlot, Sandrine. "Dynamin-Mediated Membrane Fission." Paris 7, 2012. http://www.theses.fr/2012PA077136.
Full textAbstract:
La cellule eukaryote est organisée en plusieurs compartiments, appelés organelles, délimités par des membranes; La fission des membranes est nécessaire pour le transport intracellulaire entre organelles. L'endocytose est un mécanisme de transport depuis la membrane plasmique vers les autres organelles. La Dynamine est une guanosine triphosphatase (GTPase) impliquée dans la fission des vésicules pendant l'endocytose médiée par la Clathrine. Elle polymerise en hélice au coup des bourgeons endocytiques. Après hydrolyse du GTP, la structure de l'hélice est modifiée : le rayon interne diminue de 10 à 5 nm et le pas hélical de 13 à 9 nm. Ces modifications indiquent un mécanisme de constriction. La dynamique de constriction est étudiée en suivant la rotation de microbilles attachées à des tubes lipidiques recouverts de Dynamine. La déformation des hélices de Dynamine est concertée et amortie par la friction entre membrane et Dynamine. Cependant la constriction ne suffit pas pour la fission. Pour comprendre davantage son mécanisme, la fission par la Dynamine est étudiée à l'aide de tubes lipidiques extraits de vésicules unilamellaires géantes. La fission se produit au bord de l'hélice, où la membrane est fortement courbée. D'après l'analyse statistique des temps de fission, la réaction de fission peut être modélisée par une unique barrière énergétique. La dépendance du temps de fission en rigidité de membrane, en tension de membrane et en couple est établie théoriquement et validée expérimentalement. Ce travail établit le profil énergétique de la réaction de fission membranaire et évalue à 70 KBT la barrière énergétiqueThe eukaryotic cell is organized in several compartments, named organelles, delimited by lipid membranes. The fission of these membranes is required for vesicular traffic between organelles. Endocytosis is the mechanism of vesicular traffic from the plasma membrane towards other organelles inside the cell. Dynamin is a guanosise triphosphatase (GTPase) implicated in vesicle scission during Clathrin-mediated endocytosis. It polymerizes into a helix at the neck of endocytic buds. Upon GTP hydrolysis, conformational changes modify the helical structure : the inner radius decreases from 10 to 5 nm and the helical pitch reduces from 13 to 9 nm. These modifications show that fission proceeds through a constriction mechanism. The dynamics of constriction is investigated by monitoring the rotations of microbeads attached along Dynamin-coated tubes after GTP addition. The deformation of Dynamic helices is highly concerted and damped by the friction between membrane and Dynamin. However constriction is not enough to trigger fission. To further understand fission, Dynamin polymerization and fission are studied on lipid tubes extruded from Giant Unilamellar Vesicles. It is shown that fission occurs at the edge of the helix, where the membrane is strongly curved. A statistical analysis of fission time reveals that the fission reaction can be modeledby a single step energy barrier. The fission time dependence on membrane tension, membrane rigidity and torque is established theoretically and validated experimentally. This work gives a quantitative picture of the energy landscape of Dynamin-mediated fission : the height of the energy barrier of fission is estimated around 70 KBT
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Ferreira, Brigham Marco Paulo. "Nonstationary Stochastic Dynamics of Neuronal Membranes." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066111/document.
Full textAbstract:
Les neurones interagissent à travers leur potentiel de membrane qui a en général une évolution temporelle complexe due aux nombreuses entrées synaptiques irrégulières reçues. Cette évolution est mieux décrite en termes probabilistes, en raison de ces entrées irrégulières ou «bruit synaptique». L'évolution temporelle du potentiel de membrane est stochastique mais aussi déterministe: stochastique, car conduite par des entrées synaptiques qui arrivent de façon aléatoire dans le temps, et déterministe, car un neurone biologique a une évolution temporelle très similaire quand soumis à une même séquence d'entrées synaptiques. Nous étudions les propriétés statistiques d'un modèle simplifié de neurone soumis à des entrées à taux variable d'où en résulte l'évolution non-stationnaire du potentiel de membrane. Nous considérons un modèle passif de membrane neuronale, sans mécanisme de décharge neuronale, soumis à des entrées à courant ou à conductance sous la forme d'un processus de «shot noise». Les fluctuations du potentiel de membrane sont aussi modélisées par un processus stochastique similaire, de «shot noise» filtré. Nous avons analysé les propriétés statistiques de ces processus dans le cadre des transformations de processus ponctuels de Poisson. Des propriétés de ces transformations sont dérivées les statistiques non-stationnaires du processus. Nous obtenons ainsi des expressions analytiques exactes pour les moments et cumulants du processus filtré dans le cas général des taux d'entrée variables. Ce travail ouvre de nombreuses perspectives pour l'analyse de neurones dans les conditions in vivo, en présence d'entrées synaptiques intenses et bruitéesNeurons interact through their membrane potential that generally has a complex time evolution due to numerous irregular synaptic inputs received. This complex time evolution is best described in probabilistic terms due to this irregular or "noisy" activity. The time evolution of the membrane potential is therefore both stochastic and deterministic: it is stochastic since it is driven by random input arrival times, but also deterministic, since subjecting a biological neuron to the same sequence of input arrival times often results in very similar membrane potential traces. In this thesis, we investigated key statistical properties of a simplified neuron model under nonstationary input from other neurons that results in nonstationary evolution of membrane potential statistics. We considered a passive neuron model without spiking mechanism that is driven by input currents or conductances in the form of shot noise processes. Under such input, membrane potential fluctuations can be modeled as filtered shot noise currents or conductances. We analyzed the statistical properties of these filtered processes in the framework of Poisson Point Processes transformations. The key idea is to express filtered shot noise as a transformation of random input arrival times and to apply the properties of these transformations to derive its nonstationary statistics. Using this formalism we derive exact analytical expressions, and useful approximations, for the mean and joint cumulants of the filtered process in the general case of variable input rate. This work opens many perspectives for analyzing neurons under in vivo conditions, in the presence of intense and noisy synaptic inputs
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Hyvönen, M. (Marja). "Molecular dynamics simulations on phospholipid membranes." Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514259432.
Full textAbstract:
Abstract
Phospholipids are the main components of cell membranes, lipoproteins and other
membrane structures in living organisms. Properties of lipid molecules are important to the
overall behaviour and interactions of membranes. Furthermore, characteristics of the
biological membranes act as important regulators of membrane functions. Molecular dynamics
(MD) simulations were applied in this thesis to study properties of biological membranes. A
certain degree of acyl chain polyunsaturation is essential for the proper functioning of
membranes, but earlier MD simulations had not addressed the effects of polyunsaturation.
Therefore a solvated all-atom bilayer model consisting of diunsaturated
1-palmitoyl-2-linoleoyl-3-phosphatidylcholine (PLPC) molecules was simulated. The analysis
of the simulation data was focused on the effects of double bonds on a membrane structure.
Self-organising neural networks were applied to the analysis of the
conformational data from the 1-ns simulation of PLPC membrane. Mapping of 1.44 million
molecular conformations to a two-dimensional array of neurons revealed, without human
intervention or requirement of a priori knowledge, the main
conformational features. This method provides a powerful tool for gaining insight into the
main molecular conformations of any simulated molecular assembly.
Furthermore, an application of MD simulations in the comparative analysis of
the effects of lipid hydrolysis products on the membrane structure was introduced. The
hydrolysis products of the phospholipase A2
(PLA2) enzyme are known to have a role in a variety of physiological
processes and the membrane itself acts as an important regulator of this enzyme. The
simulations revealed differences in the bilayer properties between the original and
hydrolysed phospholipid membranes. This study provides further evidence that MD simulations
on biomembranes are able to provide information on the properties of biologically and
biochemically important lipid systems at the molecular level.
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Ries, Jonas. "Advanced Fluorescence Correlation Techniques to Study Membrane Dynamics." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1219846317196-73420.
Full textAbstract:
Fluorescence Correlation Spectroscopy (FCS) is a powerful tool to measure important physical quantities such as concentrations, diffusion coefficients, diffusion modes or binding parameters, both in solution and in membranes. However, it can suffer from severe artifacts, especially in non-ideal systems. Here we develop several novel implementations of FCS which overcome these limitations and facilitate accurate and quantitative determination of dynamic parameters in membranes. Two-focus FCS with camera-detection allows for accurate and calibration-free determination of diffusion coefficients. Confocal FCS using a laser scanning microscope provides an unprecedented positioning accuracy which enabled us to study, for the first time with FCS, dynamics in bacterial membranes. Scanning FCS with a scan path perpendicular to the membrane plane allows to correct for instabilities permitting long measurement times necessary to study slow diffusion. It can easily be extended to measure calibration-free diffusion coefficients with two-focus scanning FCS and to quantify binding with dual color scanning FCS. Spectral crosstalk can be avoided effectively by using alternating excitation. Using this method we were able to perform measurements in systems previously not accessible with FCS, such as yeast cell membranes or membranes of living zebrafish embryos. Line-scan FCS with a scan path in the membrane plane uses the parallel acquisition along the line to increase the statistical accuracy and decrease the measurement times. Knowledge of the scan speed serves as an internal calibration, enabling accurate diffusion and concentration measurements within seconds, hardly affected by photobleaching. Both realizations of scanning FCS can be easily implemented with commercial laser scanning microscopes. Often, a fluorescence background around the membrane cannot be avoided. The high surface selectivity needed in this case can be achieved efficiently by using a novel objective for FCS, the supercritical angle objective, which produces a very flat and laterally confined detection volume. Another technique with similar surface selectivity is FCS with total internal reflection excitation (TIRFCS). Due to the lack of a correct model, the accurate analysis of TIR-FCS data was previously not possible. In this work we develop such a model, enabling quantitative measurements of membrane dynamics with TIR-FCS. The novel FCS techniques developed here will have a high impact on the use of FCS to address key questions in biological systems, previously inaccessible by other methodsFluoreszenz-Korrelations-Spektroskopie (FCS) ist eine mächtige Methode, um wichtige physikalische Parameter wie Konzentrationen, Diffusionskoeffizienten, Diffusionsarten oder Bindungsparameter in Lösung und in Modell- oder Zellmembranen zu bestimmen. In nichtidealen Systemen ist FCS fehleranfällig. In dieser Arbeit entwickeln wir mehrere neuartige Realisierungen von FCS, welche diese Fehlerquellen umgehen und die genaue und quantitative Messung dynamischer Parameter in Membranen ermöglichen. Zwei-Fokus FCS mit Kamera-Detektion erlaubt eine genaue und kalibrationsfreie Messung von Diffusionskoeffizienten. Konfokale FCS mit einem Laserscanningmikroskop besitzt eine bislang unerreichte Positionsgenauigkeit, welche uns erstmals dynamische Messungen in Bakterienmembranen mit FCS ermöglichte. Scanning FCS mit einem Scanweg senkrecht zur Membran ermöglicht eine Korrektur von Instabilitäten und damit lange Messzeiten, die zur Bestimmung langsamer Diffusionskoeffizienten notwendig sind. Eine Erweiterung zur kalibrationsfreien Messung von Diffusionskoeffizienten mit Zwei-Fokus Scanning FCS und von Bindungsparametern mit Zwei-Farben Scanning FCS ist einfach. Mit diesen Methoden konnten wir in Systemen messen, die bislang FCS nicht zugänglich waren, so in Hefezellmembranen oder in Membranen lebender Zebrafischembryonen. Line-scan FCS besitzt einen Scanweg parallel zur Membran. Die parallele Messung entlang der ganzen Linie führt zu einer deutlichen Verbesserung der Statistik und damit zu kurzen Messzeiten. Die Kenntnis der Scangeschwindigkeit dient einer internen Kalibration und erlaubt eine akkurate Bestimmung von Diffusionskoeffizienten und Konzentrationen innerhalb weniger Sekunden, kaum beeinflusst vom Bleichen von Fluorophoren. Beide Arten von Scanning FCS können mit einem kommerziellen Laserscanningmikroskop realisiert werden. Häufig kann bei FCS Messungen ein fluoreszierender Hintergrund nicht vermieden werden. Hier ist eine hohe Oberflächenselektivitiät nötig, welche effizient mit einem neuartigen Objektiv erreicht werden kann. Dieses Supercritical Angle-Objektiv erzeugt ein sehr flaches und lateral begrenztes Detektionsvolumen. Eine weitere Methode mit einer ähnlich guten Oberflächenselektivität ist FCS mit Anregung über totale interne Reflektion (TIR-FCS). Bislang war eine quantitative Analyse der TIR-FCS Daten kaum möglich, da keine ausreichend genaue theoretische Beschreibung existierte. In dieser Arbeit entwickeln wir ein akkurates Modell, welches quantitative Messungen mit TIR-FCS erlaubt. Die hier entwickelten neuartgien FCS-Techniken ermöglichen die Untersuchung biologischer Fragestellungen, welche bislang keiner anderen Methode zugänglich sind
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Brandt, Erik G. "Molecular Dynamics Simulations of Fluid Lipid Membranes." Doctoral thesis, KTH, Teoretisk biologisk fysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-42586.
Full textAbstract:
Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted.QC 20111014
Modelling of biological membranes