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This thesis describes studies on nanohybrid systems consisting of single-walled carbon nanotubes (SWNTs) with monolayer coatings of semiconducting polymers. Steady-state and time-resolved optical and high-resolution microscopy experiments were used to investigate the blends. These materials show promise for use in organic photovoltaics (OPVs) owing to the high carrier mobilities and large aspect ratios of SWNTs, the controllable solubilisation of tubes with various polymers and the broad light-harvesting abilities of organic polymers. Chapters 1 and 2 introduce the theory and background behind the work and present a literature review of previous work utilising carbon nanotubes in OPV devices, revealing poor performances to date. The experimental methods used during the thesis are detailed in Chapter 3 and the solution processing techniques used to prepare the polymer–nanotube blend samples are described in Chapter 4. Chapter 5 describes a study on a nanotube blend with a thiophene polymer, a system previously unsuccessfully implemented into OPV devices. Ultrafast spectroscopic measurements showed that electrons can transfer on a 400 fs time scale from the polymer to nanotubes and the conditions to allow long-lived free charges to be produced were found. The study is extended in Chapter 6 to show that nanostructures consisting of a nanotube coated in one polymer can then be coated by a second polymer and that these nano-engineered structures could be implemented into OPV devices. The use of a competition binding process to isolate purely semiconducting nanotubes dispersed with any desired polymer is then described in Chapter 7. Finally, Chapter 8 introduces systems consisting of chains of porphyrin units, nature’s light-harvesting systems, bound to nanotubes and the blends were found to exhibit the required electronic alignment for use in OPVs. The work described in this thesis provides an explanation for the poor device behaviour of nanotube–polymer blends to date and, in particular, demonstrates several nanohybrid systems that show particular promise for improved OPV applications.

The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance. The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic Π-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems. Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor. Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed. The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.

The centriole is a complex cylindrical assembly found in the cells of ciliated eukaryotes. It serves two important roles in the cell: templating the growth of cilia, and forming the basis of the centrosome, which is the major microtubule organising centre in the cell. Cilia and centrosomes are involved in many cellular processes, from signalling to cell division and differentiation. As such, defects in centriole assembly can have downstream consequences on these processes and are linked to a variety of human diseases including cancer and microcephaly. The complex superstructure of the centriole has fascinated biologists for decades. It comprises a nine-fold, radially symmetric array of microtubule triplet blades attached to a central cartwheel structure. During the last two decades, proteomic analyses have identified many proteins that are associated with the centriole. However, genetic studies have shown that only a surprisingly small number of these proteins are essential for the biogenesis of the centriole. In Drosophila melanogaster, three such essential proteins, SAS-6, Ana2 and SAS-4 are required in the early stages of centriole biogenesis. In this thesis I have investigated the assembly steps involving these key players from a structural perspective. I have identified and recombinantly expressed functional domains of these proteins in order to characterise them in vitro. Using X-ray crystallography and other biophysical techniques, I have been able to define mechanisms for several steps involved in the assembly of these proteins. In collaboration with colleagues in the laboratory I have been able to investigate the biological significance of these essential assembly steps in vivo. This information has provided novel insights into the molecular, and even atomic, detail of the initial steps of centriole assembly, including an explanation of a natural point mutation involved in human microcephaly.

This work has been a study of systems, mostly of sulfa-drugs, showing polymorphic behaviour. Using different means as solid state NMR, X-ray analysis, and theoretical calculations, we have seen how it is possible to understand results obtained from the different techniques, proving how the study of polymorphic systems needs cooperative advice from the different techniques that are able to detect polymorphic differences. Within the sulfa-drugs I have been mostly concentrating on sulfanilamide, studying (^13)C and (^15)N solid state NMR spectra of the different polymorphs. The NMR parameters that have been most interesting to study, have been the relaxation times that have revealed complicated motion of the molecule despite it being a small molecule. In order to obtain detailed information from (^15)N spectra it has been necessary to enrich the samples and this has enabled a study of the shielding tensors of the nitrogens in the molecule. (^13)C spectra were also recorded of systems studied sulfathiazole solvates that proved to show some of the same solid state effects in the NMR spectra as sulfanilamide. Shielding calculations have proved to be still limited in order to obtain reliable information on the shielding of both and (^13)C (^15)N nuclei but considering hydrogen-bonded molecules, as opposed to isolated molecules, seemed to have improved the calculations quite a lot, so that some idea of intermolecular effects could be deducted. Exact positions of the hydrogen has proved to be essential as well in order to improve the calculations. Finally a case study for the REDOR pulse sequence has been carried out. Different attempts to understand the effects influencing this particular experiment have been carried out on 20% and 99% doubly enriched glycine, as well as on a particular sample, doubly enriched BRL55834, but the internuclear distances measured with this technique still displayed some uncertainties that made results not thoroughly reliable.

This thesis describes a comprehensive study of understanding the mechanism of rigidity sensing by quantitative analysis using submicron pillar array substrates. From mechanobiology perspective, we explore and study molecular pathways involved in rigidity and force sensing at cell-matrix adhesions with regard to cancer, regeneration, and development by quantification methods. In Chapter 2 and 3, we developed fabrication and imaging techniques to enhance the performance of a submicron pillar device in terms of spatial and temporal measurement ability, and we discovered a correlation of rigidity sensing forces and corresponding proteins involved in the early rigidity sensing events. In Chapter 2, we introduced optical effect arising from submicron structure imaging, and we described a technique to identify the correct focal plane of pillar tip by fabricating a substrate with designed-offset pillars. From calibration result, we identified the correct focal plane that was previously overlooked, and verified our findings by other imaging techniques. In Chapter 3, we described several techniques to selectively functionalize elastomeric pillars top and compared these techniques in terms of purposes and fabrication complexity. Techniques introduced in this chapter included direct labeling, such as stamping of fluorescent substances (organic dye, nano-diamond, q-dot) to pillars top, as well as indirect labeling that selectively modify the surface of molds with either metal or fluorescent substances. In Chapter 4, we examined the characteristics of local contractility forces and identified the components formed a sarcomere like contractile unit (CU) that cells use to sense rigidity. CUs were found to be assembled at cell edge, contain myosin II, α-actinin, tropomodulin and tropomyosin (Tm), and resemble sarcomeres in size (~2 μm) and function. Then we performed quantitative analysis of CUs to evaluate rigidity sensing activity over ~8 hours time course and found that density of CUs decrease with time after spreading on stiff substrate. However addition of EGF dramatically increased local contraction activity such that about 30% of the total contractility was in the contraction units. This stimulatory effect was only observed on stiff substrate not on soft. Moreover, we find that in the early interactions of cells with rigid substrates that EGFR activity is needed for normal spreading and the assembly of local contraction units in media lacking serum and any soluble EGF. In Chapter 5, we performed high temporal- and spatial-resolution tracking of contractile forces exerted by cells on sub-micron elastomeric pillars. We found that actomyosin-based sarcomere-like CUs simultaneously moved opposing pillars in net steps of ~2.5 nm, independent of rigidity. What correlated with rigidity was the number of steps taken to reach a force level that activated recruitment of α-actinin to the CUs. When we removed actomyosin restriction by depleting tropomyosin 2.1, we observed larger steps and higher forces that resulted in aberrant rigidity sensing and growth of non-transformed cells on soft matrices. Thus, we conclude that tropomyosin 2.1 acts as a suppressor of growth on soft matrices by supporting proper rigidity sensing.

Malgré un large éventail d'applications de la gélatine et en dépit de son utilisation très ancienne, sa composition et sa structure ne sont pas encore entièrement connues et comprises. La gélatine est obtenue à partir de tissus animaux (peaux ou os) et est le résultat de l'hydrolyse partielle du collagène. La production de gélatine la plus abondante est celle de peau de porc qui représentait 46% de la production totale en 2007. Parmi les nombreuses applications, la gélatine de peau de porc est utilisée comme ingrédient principal des gélules dures pour l'industrie pharmaceutique. Une propriété importante de ces gélules est qu'elles fondent dans l'eau à une température au-dessus de 30° C et libèrent facilement les médicaments qu’elles contiennent dans le tube digestif. Les gélules dures doivent répondre à des spécifications de dissolution strictes tout au long de leur durée de conservation d'environ cinq ans. Ainsi, un test de dissolution dans l'eau est appliqué à la gélatine artificiellement vieillie dans des conditions de température et d'humidité élevées. Bien qu'avant le vieillissement le taux de dissolution de la gélatine corresponde toujours aux besoins de l'industrie pharmaceutique, une grande variabilité du taux de dissolution est observée après vieillissement. De plus, cette variabilité de dissolution dépend de l'origine de production de la gélatine. Dans ce contexte, un premier objectif était de comprendre les mécanismes sous-jacents impliqués dans la variabilité de la qualité de dissolution de la gélatine de peau de porc. Un deuxième objectif était d'identifier d'éventuels "marqueurs" de la dissolution de la gélatine afin de prédire son comportement au cours du vieillissement. Trois différents sites de production ont été choisis: deux en Europe et un aux USA. Au cours du vieillissement, la formation de cross-links a été mise en évidence et parmi ces cross-links, la dityrosine a été identifiée comme marqueur du vieillissement. En outre, les taux d'amines et d'aldéhydes ont diminué. Etant donné que ces deux fonctions sont connues pour réagir ensemble; ce résultat suggère qu'elles pourraient former d'autres cross-links au cours du vieillissement. Le processus d'oxydation dans la gélatine a été clairement démontré. De plus, la quantité de triple-hélices et leur stabilité au chauffage ont diminué alors que la quantité de conformation aléatoire et, probablement, de boucles-β augmente. Les résultats ont mis en évidence que l'origine de production affecte la composition chimique de la gélatine. Par exemple, la quantité de cross-links formés, comme la dityrosine, dans les gélatines fraîches et vieillies, différait selon l'origine de production. Nous avons également pu souligner que l'environnement physico-chimique de l'arginine permettait de distinguer l'origine de production de la gélatine. En ce qui concerne la dissolution de la gélatine, celles présentant des taux de dissolution non conformes avaient plus de phase amorphe après vieillissement que les gélatines conformes. L'implication des lipides dans la diminution de la dissolution de la gélatine a également été mise en évidence. La haute teneur en fer était également liée à la diminution de la dissolution mais seulement dans un site de production, ce qui suggère que la variabilité de dissolution a probablement des causes multifactorielles et dépendantes de l'origine de production.Avec le dichroïsme circulaire, nous avons pu discriminer les gélatines conformes des non-conformes avant même le vieillissement de ces gélatines. Cependant, l'interprétation des résultats reste très difficile en raison du manque d'information dans la littérature. Un tel résultat est important pour prédire le comportement de la gélatine avant le vieillissement. De manière générale, nos résultats ont mis en évidence qu’il serait pertinent de contrôler et de réduire le niveau d'oxydation et la teneur en lipides de la gélatine pour diminuer sa variabilité de dissolution. (...) / Despite a wide range of applications of gelatin and despite its very former use, gelatin composition and structure remains not fully known and understood. It is derived from animal tissue (skins or bones) and is the result of partial hydrolysis of collagen. The most abundant gelatin production, which is the focus of the present work, is pig skin gelatin which represented 46% of total production in 2007. Among numerous applications, gelatin is used as the main ingredient of the hard capsules for the pharmaceutical industry. An important property of hard capsules is that they melt in water at a temperature above 30°C and easily release drugs in the human digestive tract. Hard capsules have to meet strict dissolution specifications all along a shelf life of about five years. Thus, a dissolution test in water is applied to the gelatin constituting the hard capsules, after being artificially aged under high temperature and humidity conditions. While before aging the dissolution rate of gelatin always fit with requirement of pharmaceutical industry, a high variability in dissolution rate is observed after aging. Moreover, this dissolution variability was shown depending on the gelatin origin of production. In this context, a first objective of this work was to understand the underlying mechanisms involved in the variability of the dissolution quality of pig skin gelatin. A second objective was to identify possible “markers” of gelatin dissolution in order to predict the behaviour of gelatin through aging. Three different sites of production were chosen: two in Europe and one in USA. Cross-links formation was evidenced during aging, and among them, dityrosine was expressly identified as a marker of aging. In addition the levels of amines and aldehydes were decreased. Given that these two functions could react together; this result suggests that they could form other cross-links. Oxidation process in gelatin was clearly demonstrated. Furthermore, the quantity of triple-helices and their stability to heating decreased while the quantity of random coil and, probably, β-turns conformations increased. The results highlighted that origin of production impacts the chemical composition of gelatin. For instance, the extent of cross-link formation, such as dityrosine, in both fresh and aged gelatins, differed according to the origin of production. It was also pointed out that the physico-chemical environment of arginine allowed the distinction of production origin of gelatin. Regarding the gelatin dissolution, those showing non-compliant dissolution rates exhibited higher content of amorphous phase after aging than compliant ones. The implication of lipids in the decrease of gelatin dissolution rate was also evidenced. The decrease in dissolution was linked to the iron content only in one production site supporting the fact that dissolution variability has probably multifactorial causes, depending on the origin of production. The compliant and non-compliant dissolution rates were discriminate even before aging of gelatins by circular dichroism. However, the results interpretation remains quite difficult due to lack of literature information.Such a result is of importance in a view of predicting the behavior of gelatin before aging. To display a general overview, our results highlighted that, in order to reduce variability in the dissolution of gelatin, controlling and reducing the oxidation level and the lipid content will be relevant levers. To study the structural conformation thoroughgoing small angles neutrons would be an interesting tool. To complete the characterization of gelatin composition, quantifying and profiling lipids and sugars would be useful to better understand the gelatin oxidative instability.

Conjugated polymers and oligomers are great materials for use in the next generation devices namely organic field effect transistors, light emitting diodes and polymeric solar cells. Apart from having the potential for developing power-efficient, flexible, robust and inexpensive devices, conjugated polymers can also be tuned by molecular design to optimize device characteristics. One key problem for the full commercial exploitation of conjugated polymers is that the charge carrier mobility of the state-of-the-art polymer semiconductors is much lower than required for many applications. The performance of the devices is strongly dependent on the molecular structure and supermolecular assembly of the conjugated polymer chains. This thesis covers our attempts to design molecular structure to control and improve the solid state properties of conjugated polymers. The relative placement of side chains along the backbone has a great influence on the solid state ordering of conjugated polymers. Poly(2,5-disubstituted-1,4-phenylene ethynylene)s (PPE)s, an important class of conjugated polymers, are generally synthesized by Pd-catalyzed coupling polymerizations of appropriately substituted diiodo and diethynyl benzenes (i.e., A-A and B-B type monomers). In asymmetrically substituted PPEs, this results in an irregular substitution pattern of the side chains along the polymer backbone. We report a new synthetic approach to prepare regioregular unsymmetrically substituted PPEs by polymerization of 4-iodophenylacetylenes (i.e., A-B type monomer). We provide a detailed discussion of various approaches to the synthesis of PPEs with different regioregularities and provide a description of the differences between regioregular and regiorandom analogs. The effect of regioregularity becomes even more important when the two side chains are very dissimilar or amphiphilic. We explore the effect of relative placement hydrophobic (dodecyloxy) / hydrophilic (tri(ethylene glycol) and hydrophobic (dodecyloxy)/fluorophilic (fluoroalkyl) side chains along the poly(1,4-phenylene ethynylene) backbone. We found that the regioregular substitution of the polymer backbone provides a structure in which the side chains segregate to afford a Janus-type structure. The regioregular polymer chains pack more densely in a monolayer at the air-water interface, and pack into a bilayer in the solid state to form a highly crystalline material. Pentacenes are very important organic molecules for use as semiconductor in oFETs due to their low band gap and high field effect mobility. One approach to reduce the bandgap of a polymeric system and improve performance is to include low bandgap small molecules into the conjugated backbone. A new copolymer system consisting of pentacene and terthiophene was developed and its optical and electronic properties along with its stability were evaluated. We report the use of ultrasonication of P3HT as a novel operationally-simple process to significantly improve the field effect mobility of P3HT-based FETs, thereby potentially eliminating the need for dielectric surface modifications or further processing of the device. Investigation of the sonicated polymer samples by number of characterization techniques indicates that ultrasonication leads to aggregation and ordering of the P3HT chains resulting in increase in the mobility.

The interfacial electronic structure of the organic material- tris(8-hydroxyquinolinato)aluminum (Alq3) forming an interface with cobalt metal has been investigated in this research. The primary characterization method used in this research was near-edge X-ray absorption fine structure (NEXAFS) spectroscopy which probes the unoccupied molecular orbitals of a material. Density functional theory (DFT) calculations have also been employed to calculate the partial density of states (PDOS) of all constituent elements present in Alq3 molecule. The DFT calculations helped to determine the molecular orbital structure of Alq3 and to understand how the orbital structure is influenced by forming an interface with ferromagnetic Co layer. The experimental NEXAFS spectra measured in total fluorescence yield (TFY) showed that the lowest unoccupied molecular orbital (LUMO) and LUMO+1 states of Alq3 were not affected by the presence of Co when Co is deposited onto Alq3. On the other hand, a charge transfer between Co and Alq3 led the loss or reduction of LUMO+2 state for a Co(top)/Alq3 bilayer sample when compared to pristine Alq3 reference sample (without Co deposition). This selective effect of Co on the orbital configuration of Alq3 suggests that Co atoms diffuse into Alq3 and interact with preferred sites in Alq3. By comparing the spectral change in the experimental NEXAFS spectra to the calculated PDOS of Alq3, the preferred interaction sites between Co and Alq3 could be successfully determined. This work suggests that the spectroscopic approach using synchrotron-radiation X-ray spectroscopy can serve as a powerful means for studying the interfacial electronic structure between magnetic metals and organic semiconductors and can contribute to the research and development of high performance organic spintronics.

Ion traps are an incredibly versatile tool which have many applications throughout the physical sciences, including such diverse topics as mass spectrometry, precision frequency metrology, tests of fundamental physics, and quantum computing. In this thesis, experiments are presented which involve trapping and measuring properties of Th³⁺. Th³⁺ ions are of unique interest in part because they are a promising platform for studying an unusually low-lying nuclear transition in the 229Th nucleus which could eventually be used as an exceptional optical clock. Here, experiments to measure electronic lifetimes of Th³⁺ are described. A second experimental topic explores the production of sympathetically cooled molecular ions. The study of cold molecular ions has a number of applications, some of which include spectroscopy to aid the study of astrophysical objects, precision tests of quantum electrodynamics predictions, and the study of chemical reactions in the quantum regime. The experiments presented here involve the production of barium monohalide ions, BaX⁺ (X = F, Cl, Br). This type of molecular ion proves to be particularly promising for cooling to the rovibrational ground state. The method used for producing BaX⁺ ions involves reactions between cold, trapped Ba⁺ ions and neutral gas phase reactants at room temperature. The Ba⁺ ion reaction experiments presented in this thesis characterize these reactions for producing Coulomb crystals composed of laser cooled Ba⁺ ions and sympathetically cooled BaX⁺ ions.