A robust algorithm for segmenting fluorescence images and its application to single-molecule counting

La microscopie par fluorescence de cellules vivantes produit de grandes quantités de données. Ces données sont composées d’une grande diversité au niveau de la forme des objets d’intérêts et possèdent un ratio signaux/bruit très bas. Pour concevoir un pipeline d’algorithmes efficaces en traitement d’image de microscopie par fluorescence, il est important d’avoir une segmentation robuste et fiable étant donné que celle-ci constitue l’étape initiale du traitement d’image. Dans ce mémoire, je présente MinSeg, un algorithme de segmentation d’image de microscopie par fluorescence qui fait peu d’assomptions sur l’image et utilise des propriétés statistiques pour distinguer le signal par rapport au bruit. MinSeg ne fait pas d’assomption sur la taille ou la forme des objets contenus dans l’image. Par ce fait, il est donc applicable sur une grande variété d’images. Je présente aussi une suite d’algorithmes pour la quantification de petits complexes dans des expériences de microscopie par fluorescence de molécules simples utilisant l’algorithme de segmentation MinSeg. Cette suite d’algorithmes a été utilisée pour la quantification d’une protéine nommée CENP-A qui est une variante de l’histone H3. Par cette technique, nous avons trouvé que CENP-A est principalement présente sous forme de dimère.

Polymer-Solvent Interaction Parameter for NR/SBR and NR/BR Blends

Polymer-solvent interaction parameters for the blends of natural rubber (NR) with styrene-butadiene rubber (SBR) and polybutadiene rubber ( BR) are calculated using the Flory-Rehner equation by equating the network density of the vulcanizates in two solvents.

A Novel Method for Switching and Tuning of PBG Structures

Photonic band-gap (PBG) structures are utilized in microwave components as filters to suppress unwanted signals. In this work, rectangular perforations were created in the ground plane of a microstrip line to construct a PBG structure. A gold-coated alumina substrate was utilized to switch or tune the bandstop characteristics of this structure. It was demonstrated that the bandstop characteristics were switched off from - 35 to - 1 dB at 16 GHz. Tuning of the bandstop edge with a shift of 1.5 GHz was also shown

Luminescence tuning and enhanced nonlinear optical properties of nanocomposites of ZnO–TiO2

In this article we present the spectral and nonlinear optical properties of ZnO–TiO2 nanocomposites prepared by colloidal chemical synthesis. Emission peaks of ZnO–TiO2 nanocomposites change from 340 nm to 385 nm almost in proportion to changes in Eg. The nanocomposites show self-defocusing nonlinearity and good nonlinear absorption behaviour. The nonlinear refractive index and the nonlinear absorption increase with increasing TiO2 volume fraction at 532 nm and can be attributed to the enhancement of exciton oscillator strength. ZnO–TiO2 is a potential nanocomposite material for the tunable light emission and for the development of nonlinear optical devices with a relatively small limiting threshold

Parameter Estimation in Minification Processes

In this article it is proved that the stationary Markov sequences generated by minification models are ergodic and uniformly mixing. These results are used to establish the optimal properties of estimators for the parameters in the model. The problem of estimating the parameters in the exponential minification model is discussed in detail.

Tuning mesoporous molecular sieve SBA-15 for the immobilization of α-amylase

The present work describes the immobilization of α-amylase over well ordered mesoporous molecular sieve SBA-15 with different pore diameters synthesized by post synthesis treatment (PST) hydrothermally after reaction at 40°C. The materials were characterized by N 2 adsorption–desorption studies, small angle X-ray diffraction, scanning electron microscopy and high resolution transmission electron microscopy. Since α-amylase obtained from Bacillus subtilis has dimensions of 35 × 40 × 70 Å it is expected that the protein have access to the pore of SBA-15 (PST-120°C) with diameter 74 Å. The pore dimension is appropriate to prevent considerable leaching. The rate of adsorption of the enzyme on silica of various pore sizes revealed the influence of morphology, pore diameter, pore volume and pH.

Propagation characteristics and wavelength tuning of amplified spontaneous emission from dye-doped polymer.

The propagation characteristics of amplified spontaneous emission (ASE) through a rhodamine 6 G-doped polymethyl methacrylate freestanding film waveguide were studied. This was done by shifting the excitation stripe horizontally along a transversely pumped waveguide. By this method, we could tune the ASE wavelength. The maximum tunability thus obtained was ~18 nm with a pump stripe length of 6 mm.

Effect of a fluctuating parameter mismatch and the associated time-scales on coupled Rossler oscillators

We study the effect of parameter fluctuations and the resultant multiplicative noise on the synchronization of coupled chaotic systems. We introduce a new quantity, the fluctuation rate Ф as the number of perturbations occurring to the parameter in unit time. It is shown that ϕ is the most significant quantity that determines the quality of synchronization. It is found that parameter fluctuations with high fluctuation rates do not destroy synchronization, irrespective of the statistical features of the fluctuations. We also present a quasi-analytic explanation to the relation between ϕ and the error in synchrony.

Structural tuning of Montmorillonite clays by pillaring: Designing of shape selective solid acid catalysts and PANI - Montmorillonite nanocomposites

Green chemistry boots eco-friendly,natural clays as catalysts in the chemical as well as in the pharmaceutical industry.Industry demands thermal stability,mechanical strength etc for the catalyst and there the modification methods becomes important.Pillaring tunes clays as efficient catalytic templates for shape selective organic synthesis.Here pillared clays are used as promising alternatives for the environmentally hazardous homogeneous catalysts in some industrially important Friedel-Crafts alkylation reactions of arenes with lower alchohols and higher olefins.The layer structure is enhanced upon pillaring and allows the nanocomposite formation with polyaniline to develop today’s nanoscale diameter devices.Present work gives an entry of pillared clays to the world of conducting composite nanofibers.

Evidence for blueshift by weak exciton confinement and tuning of bandgap in superparamagnetic nanocomposites

Superparamagnetic nanocomposites based on Y-Fe2O3 and sulphonated polystyrene were synthesised by ion-exchange process and the structural characterisation has been carried out using X-ray diffraction technique. Doping of cobalt in to the Y-Fe2O3 lattice was effected in situ and the doping was varied in the atomic percentage range 1–10. The optical absorption studies show a band gap of 2.84 eV, which is blue shifted by 0.64 eV when compared to the reported values for the bulk samples (2.2 eV). This is explained on the basis of weak quantum confinement. Further size reduction can result in a strong confinement, which can yield transparent magnetic nanocomposites because of further blue shifting. The band gap gets red shifted further with the addition of cobalt in the lattice and this red shift increases with the increase in doping. The observed red shift can be attributed to the strain in the lattice caused by the anisotropy induced by the addition of cobalt. Thus, tuning of bandgap and blue shifting is aided by weak exciton confinement and further red shifting of the bandgap is assisted by cobalt doping.

First principles LDA+U and GGA+U study of cerium oxides: Dependence on the effective U-parameter

The electronic structure and properties of cerium oxides (CeO2 and Ce2O3) have been studied in the framework of the LDA+U and GGA(PW91)+U implementations of density functional theory. The dependence of selected observables of these materials on the effective U parameter has been investigated in detail. The examined properties include lattice constants, bulk moduli, density of states, and formation energies of CeO2 and Ce2O3. For CeO2, the LDA+U results are in better agreement with experiment than the GGA+U results whereas for the computationally more demanding Ce2O3 both approaches give comparable accuracy. Furthermore, as expected, Ce2O3 is much more sensitive to the choice of the U value. Generally, the PW91 functional provides an optimal agreement with experiment at lower U energies than LDA does. In order to achieve a balanced description of both kinds of materials, and also of nonstoichiometric CeO2¿x phases, an appropriate choice of U is suggested for LDA+U and GGA+U schemes. Nevertheless, an optimum value appears to be property dependent, especially for Ce2O3. Optimum U values are found to be, in general, larger than values determined previously in a self-consistent way.

On tuning the orientation of grains of spray pyrolysed ZnO thin films

Effect of varying spray rate on the structure and optoelectronic properties of spray pyrolysed ZnO film is analysed. ZnO films were characterised using different techniques such as X-ray diffraction (XRD), photoluminescence, electrical resistivity measurement, and optical absorption. The XRD analysis proved that, with the increase in spray rate, orientation of the grains changed from (1 0 1) plane to (0 0 2) plane. The films exhibited luminescence in two regions—one was the ‘near band-edge’ (NBE) (∼380 nm) emission and the other one was the ‘blue-green emission’ (∼503 nm). Intensity of the blue-green emission decreased after orientation of grains shifted to (0 0 2) plane. Scanning electron microscope (SEM) analysis of the films asserts that spray rate has major role in improving the crystallographic properties of the films. Moreover resistivity of the films could be lowered to 2.4×10−2 cm without any doping or post-deposition annealing

Low-Cost Micromechanically Tunable Optical Devices: Strained Resonator Engineering, Technological Implementation and Characterization

The rapid growth of the optical communication branches and the enormous demand for more bandwidth require novel networks such as dense wavelength division multiplexing (DWDM). These networks enable higher bitrate transmission using the existing optical fibers. Micromechanically tunable optical microcavity devices like VCSELs, Fabry-Pérot filters and photodetectors are core components of these novel DWDM systems. Several air-gap based tunable devices were successfully implemented in the last years. Even though these concepts are very promising, two main disadvantages are still remaining. On the one hand, the high fabrication and integration cost and on the other hand the undesired adverse buckling of the suspended membranes. This thesis addresses these two problems and consists of two main parts: • PECVD dielectric material investigation and stress control resulting in membranes shape engineering. • Implementation and characterization of novel tunable optical devices with tailored shapes of the suspended membranes. For this purposes, low-cost PECVD technology is investigated and developed in detail. The macro- and microstress of silicon nitride and silicon dioxide are controlled over a wide range. Furthermore, the effect of stress on the optical and mechanical properties of the suspended membranes and on the microcavities is evaluated. Various membrane shapes (concave, convex and planar) with several radii of curvature are fabricated. Using this resonator shape engineering, microcavity devices such as non tunable and tunable Fabry-Pérot filters, VCSELs and PIN photodetectors are succesfully implemented. The fabricated Fabry-Pérot filters cover a spectral range of over 200nm and show resonance linewidths down to 1.5nm. By varying the stress distribution across the vertical direction within a DBR, the shape and the radius of curvature of the top membrane are explicitely tailored. By adjusting the incoming light beam waist to the curvature, the fundamental resonant mode is supported and the higher order ones are suppressed. For instance, a tunable VCSEL with 26 nm tuning range, 400µW maximal output power, 47nm free spectral range and over 57dB side mode suppresion ratio (SMSR) is demonstrated. Other technologies, such as introducing light emitting organic materials in microcavities are also investigated.

Micro-electromechanical structural design and optimization of vertical cavity photonic devices with wide continuous tuning

Diese Arbeit umfaßt das elektromechanische Design und die Designoptimierung von weit durchstimmbaren optischen multimembranbasierten Bauelementen, mit vertikal orientierten Kavitäten, basierend auf der Finiten Element Methode (FEM). Ein multimembran InP/Luft Fabry-Pérot optischer Filter wird dargestellt und umfassend analysiert. In dieser Arbeit wird ein systematisches strukturelles Designverfahren dargestellt. Genaue analytische elektromechanischer Modelle für die Bauelemente sind abgeleitet worden. Diese können unschätzbare Werkzeuge sein, um am Anfang der Designphase schnell einen klaren Einblick zur Verfügung zu stellen. Mittels des FEM Programms ist der durch die nicht-lineare Verspannung hervorgerufene versteifende Effekt nachgeforscht und sein Effekt auf die Verlängerung der mechanischen Durchstimmungsstrecke der Bauelemente demonstriert worden. Interessant war auch die Beobachtung, dass die normierte Relation zwischen Ablenkung und Spannung ein unveränderliches Profil hat. Die Deformation der Membranflächen der in dieser Arbeit dargestellten Bauelementformen erwies sich als ein unerwünschter, jedoch manchmal unvermeidbarer Effekt. Es zeigt sich aber, dass die Wahl der Größe der strukturellen Dimensionen den Grad der Membrandeformation im Falle der Aktuation beeinflusst. Diese Arbeit stellt ein elektromechanisches in FEMLAB implementierte quasi-3D Modell, das allgemein für die Modellierung dünner Strukturen angewendet werden kann, dar; und zwar indem man diese als 2D-Objekte betrachtet und die dritte Dimension als eine konstante Größe (z.B. die Schichtdicke) oder eine Größe, welche eine mathematische Funktion ist, annimmt. Diese Annahme verringert drastisch die Berechnungszeit sowie den erforderlichen Arbeitsspeicherbedarf. Weiter ist es für die Nachforschung des Effekts der Skalierung der durchstimmbaren Bauelemente verwendet worden. Eine neuartige Skalierungstechnik wurde abgeleitet und verwendet. Die Ergebnisse belegen, dass das daraus resultierende, skalierte Bauelement fast genau die gleiche mechanische Durchstimmung wie das unskalierte zeigt. Die Einbeziehung des Einflusses von axialen Verspannungen und Gradientenverspannungen in die Berechnungen erforderte die Änderung der Standardimplementierung des 3D Mechanikberechnungsmodus, der mit der benutzten FEM Software geliefert wurde. Die Ergebnisse dieser Studie zeigen einen großen Einfluss der Verspannung auf die Durchstimmungseigenschaften der untersuchten Bauelemente. Ferner stimmten die Ergebnisse der theoretischen Modellrechnung mit den experimentellen Resultaten sehr gut überein.