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This thesis presents the synthesis methods and the characterizations of magnetic Fe3O4 nanoparticles, silica spheres with Fe3O4 nanoparticles embedded, and three dimensional magnetic photonic crystals (MPCs) prepared from the spheres. The structure, material composition, magnetic and optical properties, photonic band gaps (PBGs), as well as how these properties depend on the concentration of the magnetic nanoparticles, are investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), vibrating sample magnetometer (VSM), superconducting quantum interference device (SQUID), Faraday rotation (FR) and optical spectrophotometers. Well-organized, face center cubic (fcc)-structured, super-paramagnetic 3D MPCs have been obtained and their PBGs are investigated through optical spectra. Fe3O4 nanoparticles are synthesized by standard co-precipitation method and a rapid mixing co-precipitation method with particle size varied from 6.6 nm to 15.0 nm at different synthesis temperature (0°C ~ 100°C). The obtained Fe3O4 nanoparticles, which show crystalline structure with superparamagnetic property, are embedded into silica spheres prepared at room temperature through a sol-gel method using the hydrolysis of tetraethyl orthosilicate (TEOS) in a base solution with different concentrations. By controlling the synthesis conditions (e.g., chemicals, the ratio of chemicals and stirring time), different size of MPC spheres in range of 75 nm to 680 nm has been obtained in a narrow distribution. The sphere suspensions in ethanol are dropped on glass substrate in the permanent magnetic field to achieve well organized 3D MPCs with (111) triangular close packed crystal plane of fcc structure parallel to the surface of substrate. From the transmission & forward scattering spectra (TF), five PBGs have been distinguished for these MPCs and they are defined as 1st, 2nd, 3rd, 4th and 5th PBGs according to the order of peaks that appear in mathematic fitting analysis. The positions (peak wavelengths) of PBGs show sphere size dependence: with the increase of the sphere size, they increase linearly. Comparing with pure SiO2 PCs at certain sphere size, the positions of PBGs for MPCs containing moderate Fe3O4 conc. (4.3 wt. %) are at longer wavelengths. On increasing the Fe3O4 conc., however, the PBGs shift back to shorter wavelength. The PBGs shift to longer or shorter wavelength is due to the combined effect of refractive index n increasing, as well as the increase of refractive index difference Δn, which are caused by the embedded Fe3O4 nanoparticles. The transmission spectra (T) with varied incidence angle of p- and s- polarized light are studied, obtaining angular dependent and polarization sensitive PBGs. It is found that with the increase of the incidence angle, the 1st PBGs shift to shorter wavelength while the 3rd ones shift to longer wavelength. High Fe3O4 conc. MPCs (6.4 wt. %) show enhancement of this angular dependence. It is also found that the PBGs show dependence on the polarize direction of incident light. Normally, at a certain incidence angle the PBGs sift more for p- polarized incident light than for s-polarized light with respect to normal incidence. This polarized dependence can also be enhanced for high Fe3O4 conc. MPCs. With a high concentration of Fe3O4 nanoparticles, the polarization sensitivity of p- and s- increased. These PBG properties indicate applications of 3D MPCs as functional optical materials, coatings, wavelength and polarization fibers for fiber optical communications devices and dielectric sensors of magnetic field, etc.. / QC 20110224

Biodesulfurization (BDS) is an alternative to hydrodesulfurization (HDS) as a method to remove sulfur from crude oil. Dibenzothiophene (DBT) was chosen as a model compound for the forms of thiophenic sulfur found in fossil fuels; up to 70% of the sulfur in petroleum is found as DBT and substituted DBTs; these compounds are however particularly recalcitrant to hydrodesulfurization, the current standard industrial method. My thesis deals with enhancing BDS through novel strains and through nanotechnology. Chapter highlights are: Chapter 2. My first aim was to isolate novel aerobic, mesophilic bacteria that can grow in mineral media at neutral pH value with DBT as the sole sulfur source. Different natural sites in Iran were sampled and I enriched, isolated and purified such bacteria. Twenty four isolates were obtained that could utilize sulfur compounds. Five of them were shown to convert DBT into HBP. After preliminary characterization, the five isolates were sent to the Durmishidze Institute of Biotechnology in Tbilisi for help with strain identification. Two isolates (F2 and F4) were identified as Pseudomonas strains, F1 was a Flavobacterium and F3 belonged to the strain of Rhodococcus. The definite identification of isolate F5 was not successful but with high probability it was a known strain. Since no new strains were apparently discovered, I did not work further in this direction. Chapter 3. In a second approach I studied the desulfurization ability of Shewanella putrefaciens strain NCIMB 8768, because in a previous investigation carried out at Cranfield University, it had been found that it reduced sulfur odour in clay. I compared its biodesulfurization activity profile with that of the widely studied Rhodococcus erythropolis strain IGTS8. However, S. putrefaciens was not as good as R. erythropolis. Chapter 4 and 5. I then turned to nanotechnology, which as a revolutionary new technological platform offers hope to solve many problems. There is currently a trend toward the increasing use of nanotechnology in industry because of its potentially revolutionary paths to innovation. I then asked how nanotechnology can contribute to enhancing the presently poor efficiency of biodesulfurization. Perhaps the most problematic difficulty is how to separate the microorganisms at the end of the desulfurization process. To make BDS more amenable, I explored the use of nanotechnology to magnetize biodesulfurizing bacteria. In other words, to render desulfurizing bacteria magnetic, I made them magnetic by decorating their outer surfaces with magnetic nanoparticles, allowing them to be separated using an external magnet. I used the best known desulfurizing bacterial strain, Rhodococcus erythropolis IGTS8. The decoration and magnetic separation worked very well. Unexpectedly, I found that the decorated cells had a 56% higher desulfurization activity compared to the nondecorated cells. I proposed that this is due to permeabilization of the bacterial membrane, facilitating the entry and exit of reactant and product respectively. Supporting evidence for enhanced permeabilization was obtained by Dr Pavel Grigoriev, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino. In Chapter 6, to optimize attachment of the nanoparticles to the surface of the bacteria I created thin magnetic nanofilms from the nanoparticles and measured the attachment of the bacteria using a uniquely powerful noninvasive optical technique (Optical Waveguide Lightmode Spectroscopy, OWLS) to quantify the attachment and determine how the liquid medium and other factors influence the process.

Les chitooligosaccharides (COS) présentent des propriétés biologiques intéressantes telles que l'activité antimicrobienne, antifongique et antitumorale. Dans ce travail, nous avons utilisé les COS pour des applications très diverses, telles que l'ingénierie des cellules neuronales (blocage de la formation du réseau périneuronal), la complexation des cations Fe2+ et Fe3+ pour la synthèse de particules supermagnatiques et enfin pour le développement de conjugués fonctionnels à base de COS. Dans le cadre de ces études en partenariat, nous avons travaillé sur l'élaboration de chitooligosaccharides à structure contrôlée afin d’étudier leurs propriétés physico-chimiques ou biologiques. Des modifications de chitooligosaccharides ont été effectuées dans ce travail de deux façons: la modification par N-substitution et la modification par le groupe aldéhyde du résidu 2,5-anhydro-D-mannofuranose (amf) à l'extrémité réductrice des chitooligosaccharides. Les premiers types de COS consistent en la désamination suivie d'une réaction de N-réacétylation afin de contrôler (partiellement) à la fois le degré moyen d'acétylation et le degré moyen de polymérisation. La seconde stratégie consiste en la synthèse de nouveaux COS fonctionnalisés à leur extrémité réductrice par amination réductrice et oximation avec différents groupes chimiques cliquables (c'est-à-dire alcyne, alcène, azide, thiol et hydrazide). En fonction des COS fonctionnalisé ciblé, différentes techniques d'analyse ont été réalisées pour analyser pleinement leurs caractéristiques structurales telles que la spectroscopie RMN, la spectrométrie de masse MALDI-TOF, la chromatographie HPLC, la spectroscopie RAMAN et la chromatographie SEC. Des structures chimiques spécifiques de chitooligosaccharides modifiés ont été étudiées dans le but de les utiliser pour moduler le réseau périneural de neurones et l'établissement de connexions synaptiques. Nous avons également montré que les COS solubles permettent la précipitation des nanoparticules supramagnétiques de Fe3O4 avec un revêtement COS en les rendant moins toxiques. Enfin, les COS fonctionnalisés à leur extrémité réductrice pourraient être des intermédiaires utiles pour le développement de nouveaux conjugués fonctionnels à base de chitosane / Chitooligosaccharides (COS) classically present several biological properties such as anti-microbial, anti-tumor and anti-fungal activity. In this work, we used COS for widely different applications, such as tissue engeneering of neuronal cells (blocking of perineuronal net formation), the complexation of iron cations (Fe2+ and Fe3+) for the synthesis of supermagnatic particle and finally for the development of advanced functional COS-based conjugates. In this partnership studies, we worked on the elaboration of controlled structure chitooligosaccharides in order to decipher their physico-chemical or biological properties. Further modification of chitooligosaccharides was performed in this thesis in two ways: modification via amine N-substitution and the modification via the 2,5-anhydro-D-mannofuranose (amf) aldehyde group located at the reducing end of chitooligosaccharides. The first COS types consist in the nitrous depolymerization followed by N-acetylation in order to (partly) control both the mean degree of N-acetylation and the degree of polymerization. The second consist in the synthesis of new COS-based building blocks functionalized at their reducing end by reductive amination and oximation with different clickable chemical groups (i.e. alkyne, alkene, azide, thiol, and hydrazide). Depending on the targeted functionalized COS, different analysis techniques were carried out to fully characterize such as NMR spectroscopy, MALDI-TOF mass spectrometry, HPLC-chromotography, RAMAN spectroscopy and SEC chromatography. Specific chitooligosaccharides were studied in the objective to use them to modulate the perineuronal net of neurons, and the establishment of synaptic connections. We also showed that water soluble COS permit the precipitation of supramagnetic Fe3O4 nanoparticles with a COS coating and succeded in decreasing their toxicity. Finally we have shown that COS-based building blocks could be useful intermediates for the development of advanced functional COS-based conjugates such as COS-b-PEG diblock copolymers