Rotaviruses (RVs) are medically significant gastrointestinal pathogens and are a leading cause of childhood mortality in many countries. The RV RNA-dependent RNA polymerase, VP1, synthesizes RNA during viral replication only in the presence of another RV protein, VP2, which comprises the innermost core shell layer of the virion. Though these VP1-VP2 interactions are essential for RV replication, the mechanism by which the core shell regulates polymerase activity remains incompletely understood. Here, we sought to identify and characterize specific regions of both VP1 and VP2 that are required for core shell dependent polymerase activity. First, we used bioinformatics approaches to analyze VP1 and VP2 sequence diversity across many RV strains and identify positional locations of critical amino acid changes within the context of known structural domains and motifs. We next tested how the identified sequence differences influenced VP2-dependent VP1 activity in vitro. These data revealed that VP1 and VP2 protein diversity correlates with functional differences between avian and mammalian RV strains. Then, we used these sequential and functional incompatibilities to map key regions of VP1 important for mediating RNA synthesis. To pinpoint critical interacting regions of VP1 and VP2, we used site directed mutagenesis to engineer several modified VP1 and VP2 proteins. Then, we employed an in vitro RNA synthesis assay to test how the introduced mutations influenced VP2-dependent VP1 activity. Altogether, our results revealed several functionally important VP1 residues critical for in vitro VP2-dependent VP1 activity, either individually or in combination with neighboring residues, including E265/L267, R614, and D971/S978/I980. Structural analyses show VP2 interactions at these surface-exposed VP1 sites, which altogether supports a direct contact model of core shell dependent RV polymerase activity. Moreover, recombinant VP1 proteins containing multiple mutations at buried residues were incapable of facilitating RNA synthesis in vitro under the assay conditions, indicating that an extensive intramolecular signaling network exists to mediate VP1 activity. Taken together, these results suggest that VP2 binding at the VP1 surface may induce intramolecular interactions critical for VP1 activity. Overall, results from these studies provide important insight into VP1-VP2 binding interface(s) that are necessary for RV replication. / Ph. D. / Rotaviruses (RVs) are clinically-significant gastrointestinal pathogens that cause severe diarrhea and dehydration in children. RVs encode a specialized polymerase enzyme, called VP1, which functions to synthesize RNA during viral replication. RNA synthesis activities of VP1 are tightly regulated by another RV protein, VP2, which comprises the innermost core shell layer of the virion. Though these VP1-VP2 interactions are essential for viral replication, the mechanism by which the core shell supports polymerase activity remains poorly understood. Here, we sought to identify and characterize specific regions of both VP1 and VP2 that are essential for polymerase activity in a test tube (i.e., in vitro). First, we analyzed VP1 and VP2 sequence diversity across many RV strains. Then, we tested how the identified sequence differences influenced VP2-dependent VP1 activation in vitro. To pinpoint critical regions of VP1 and VP2, we next engineered and assayed several mutant proteins. Altogether, our results revealed several functionally important residues of VP1 and VP2, which raises new ideas about VP1-VP2 binding interface(s) that are important for viral replication. Moreover, results from these studies may provide a scientific platform for the rational design of next-generation RV vaccines or antiviral therapeutics.

Yes / Highly-branched poly(N-isopropyl acrylamide)s in water pass through coil-to-globule transitions. Using calorimetry and the colour change of a solvatochromic dye within the polymer, we show that some compositions have biphasic core–shell morphologies, with globular cores and open coil shells. The two-phase structure is favoured by increased branching and arises because the chain ends penetrate only to a limited degree into the polymer coil.

Lanthanide-based nanoparticles are of interest for optical displays, catalysis, telecommunication, bio-imaging, magnetic resonance imaging, multimodal imaging, etc. These applications are possible partly because the preparation of lanthanide-based nanoparticles has made tremendous progress. Now, nanoparticles are routinely being made with a good control over size, crystal phase and even shape. Despite the achievements, little attention is given to the fundamental physical chemistry aspects, such as crystal structure, architecture, cation exchange, etc. The results of the study on the crystal structures of LnF3 nanoparticles show that the middle GdF3 and EuF3 nanoparticles have two crystal phases, which has then been tuned by doping with La3+ ions. However, the required doping level is very different from the bulk. While the results for the bulk are well explained by thermodynamic calculations, kinetics is actually responsible for the results of the undoped and doped GdF3 and EuF3 nanoparticles. The attempt to make LnF3 core-shell nanoparticles led to the finding of cation exchange, a phenomenon that upon exposure of LnF3 nanoparticles to an aqueous solution containing Ln3+ ions, the Ln3+ ions in the nanoparticles are replaced by the Ln3+ ions in the solution. The consequence of the cation exchange is that LnF3 core-shell nanoparticles are unlikely to form in aqueous media using a core-shell synthesis procedure. It has also been verified that nanoparticles synthesized using an alloy procedure do not always have an alloy structure. This means that the core-shell and alloy structure of nanoparticles in the literature may not be true. The investigation of the architecture of nanoparticles synthesized in aqueous media is extended to those synthesized in organic media. The dopant ion distribution in NaGdF4 nanoparticles has been examined. It has been found that they don’t have the generally assumed statistical dopant distribution. Instead, they have a gradient structure with one type of Ln3+ ions more concentrated towards the center and the other type more concentrated towards the surface of the nanoparticles. With the understanding of these physical insights, lanthanide-based core-shell nanoparticles are prepared using the cation exchange. These core-shell nanoparticles containing a photoluminscent core and a paramagnetic shell are promising candidates for multimodal imaging. / Graduate

A size-selected series of water-soluble luminescent Ag–In–S (AIS) and core/shell AIS/ZnS QDs were produced by a precipitation technique. Up to 10–11 fractions of size-selected AIS (AIS/ZnS) QDs emitting in a broad color range from deep-red to bluish-green were isolated with the photoluminescence (PL) quantum yield reaching 47% for intermediate fractions. The size of the isolated AIS (AIS/ZnS) QDs varied from ~2 nm to ~3.5 nm at a roughly constant chemical compo- sition of the particles throughout the fractions as shown by the X-ray photoelectron spectroscopy. The decrease of the mean AIS QD size in consecutive fractions was accompanied by an increase of the structural QD imperfection/disorder as deduced from a notable Urbach absorption “tail” below the fundamental absorption edge. The Urbach increased from 90–100 meV for the largest QDs up to 350 meV for the smallest QDs, indicating a broadening of the distribution of sub-bandgap states. Both the Urbach energy and the PL bandwidth of the size-selected AIS QDs increased with QD size reduction from 3–4 nm to ~2 nm and a distinct correlation was observed between these parameters. A study of size-selected AIS and AIS/ZnS QDs by UV photoelectron spectroscopy on Au and FTO substrates revealed their valence band level EVB at ~6.6 eV (on Au) and ~7 eV (on FTO) and pinned to the Fermi level of conductive substrates resulting in a masking of any possible size- dependence of the valence band edge position.

V práci je zkoumán vliv podmínek na průběh hydrolýzy alkoxidů titanu a vlastností připravovaných nanočástic oxidu titaničitého s důrazem na teplotu a množství vody přítomné v systému. Připravované hydrolyzáty alkoxidů titanu a nanočástice oxidu titaničitého připravené z hydrolyzátů jsou studovány metodami XRD, DTA – TGA, SEM – EDS, BET a PCCS. Nanočástice magnetitu byly syntetizovány pomocí precipitační reakce z roztoku Mohrovy soli a jejich krystalová struktura, velikost a povrchové vlastnosti byly sledovány s vyhodnocením vlivu teploty a při modifikaci povrchu polykarboxyletherovým superplastifikátorem. Pro upevnění TiO2 na povrch magnetitu byla použita kombinovaná metoda aplikace vybraných nanočástic TiO2 s hydrolýzou TiO2 pomocí alkoxidů titanu za účelem přípravy fotokatalyticky aktivního core-shell práškového katalyzátoru s vylepšenými vlastnostmi adsorpce na povrchu. Studovány byly možnosti aplikace TiO2 na povrch Mn-Zn feritu, kdy byl studován vliv depozice tenkých vrstev C a Au na morfologii povrchu. Fotokatalytická aktivita vybraných připravených materiálů byla studována pomocí dekompozice methylenové modři v roztoku a par isopropanolu a ethanolu rozkládaných pomocí Mn-Zn feritu v experimentálním chemickém reaktoru s magnetickým polem stabilizovaným ložem nosiče katalyzátoru.

Polyketides are natural products with complex chemical structures and immense pharmaceutical potential that are synthesized via secondary metabolic pathways. The in-vitro synthesis of these molecules requires high supply of building blocks such as acetyl Co-enzyme A, and cofactors (adenosine triphosphate (ATP). These precursor and cofactor are synthesized from respective soluble enzymes. Owing to the expensive nature of the enzymes, it is important to immobilize enzymes to improve the process economics by enabling multiple uses of catalyst and improving overall productivity and robustness. The polymer-based particles of nano and submicron size have become attractive material for their role in the life sciences. With the advances in synthetic protocols of the microgels and commercial availability of many of the monomers, it is feasible to tune the properties of the particles as per the process requirement. The core shell microgel with functional shell allows high loading of ligands onto the microgel particles due to increased availability of functional group on the outer surface. The aim of the thesis thus was to study biochemical reactions on the smart microgels support using single (acetyl CoA synthetase (Acs)) and dual (pyruvate kinase (Pk) and L-lactic dehydrogenase (Ldh)) enzyme/s systems. The study indicated that the enzyme immobilization significantly depends on the enzyme, conjugation strategy and the support. The covalent immobilization provides rigidity to the enzyme structure as in case of Acs immobilized on PNIPAm-AEMA microgels but at the same time leads to loss in enzyme activity. Whereas, in the case of covalent immobilization of Ldh on microgel showed improved in enzyme activity. On the other hand adsorption of the enzyme via ionic interaction provide better kinetic profile of enzymes hence the membrane reactor was prepared using PNIPAm-PEI conjugates for acetyl CoA synthesis. The better outcome of work with PNIPAm-PEI resulted in its further evaluation for dual enzyme system. This work is unique in the view that the immobilization strategies were well adapted to immobilize single and dual enzymes to achieve stable bioconjugates for their respective applications in precursor biosynthesis (Acetyl Co enzyme A) and co-factor dependent processes (ACoA and ATP). The positive end results of microgels as the support (particles in solution and as the thin film (membrane)) opens further prospective to explore these systems for other precursor biomolecule production.

A size-selected series of water-soluble luminescent Ag–In–S (AIS) and core/shell AIS/ZnS QDs were produced by a precipitation technique. Up to 10–11 fractions of size-selected AIS (AIS/ZnS) QDs emitting in a broad color range from deep-red to bluish-green were isolated with the photoluminescence (PL) quantum yield reaching 47% for intermediate fractions. The size of the isolated AIS (AIS/ZnS) QDs varied from ~2 nm to ~3.5 nm at a roughly constant chemical compo- sition of the particles throughout the fractions as shown by the X-ray photoelectron spectroscopy. The decrease of the mean AIS QD size in consecutive fractions was accompanied by an increase of the structural QD imperfection/disorder as deduced from a notable Urbach absorption “tail” below the fundamental absorption edge. The Urbach increased from 90–100 meV for the largest QDs up to 350 meV for the smallest QDs, indicating a broadening of the distribution of sub-bandgap states. Both the Urbach energy and the PL bandwidth of the size-selected AIS QDs increased with QD size reduction from 3–4 nm to ~2 nm and a distinct correlation was observed between these parameters. A study of size-selected AIS and AIS/ZnS QDs by UV photoelectron spectroscopy on Au and FTO substrates revealed their valence band level EVB at ~6.6 eV (on Au) and ~7 eV (on FTO) and pinned to the Fermi level of conductive substrates resulting in a masking of any possible size- dependence of the valence band edge position.

This thesis explores how the carrier dynamics within semiconductor nanocrystals can be directly engineered through specific core-shell design. Emphasis is placed on how material characteristics, such as strain or alloying at a core-shell interface, can influence the exciton energies and the recombination dynamics within semiconductor nanocrystals. This study synthesises type-II heterojunction ZnTe/ZnSe core-shell nanocrystals via a diethyl zinc-free synthesis method, producing small size distributions and quantum yields as high as 12%. It was found that the 7% lattice mismatch between the core and shell materials places limitations on the range of structures in which coherent growth is achieved. By developing compositional and strained atomistic core-shell models a variety of physical and optical properties could be simulated and has led to a clear picture of the core-shell architecture to be built. This characterisation provides evidence that the low bulk modulus ZnTe cores are compressed by the higher bulk modulus smaller lattice constant ZnSe shells. Further studies show how strain is manifested in structures with 'sharp' core-shell interfaces and how intentional alloying the interface can influence the growth and exciton energies. A (2-6)-band effective mass model was able to distinguish between the as-grown 'sharp' and 'alloyed' interfaces which indicated that strain accentuates the redshift of the excitonic state whilst reduced strain within an alloyed interface sees a reduced redshift. Single nanocrystal spectroscopy investigations of brightly emitting single graded alloyed nanocrystals and of a size series of commercially available CdSe/ZnS nanocrystals showed almost no fluorescence intermittency (nearly 'non-blinking'). These investigations also identified trion recombination as the main mechanism within the blinking 'off' state. Ultimately this thesis adds to the growing understanding of how specific core-shell architectures manipulate the electronic structure and develops techniques to identify specific material characteristics and how these characteristics influence the physical and optical properties within semiconductor nanocrystals.

Doctor of Philosophy / Department of Mechanical and Nuclear Engineering / Gurpreet Singh / Molecular precursor derived ceramics (also known as polymer-derived ceramics or PDCs) are high temperature glasses that have been studied for applications involving operation at elevated temperatures. Prepared from controlled thermal degradation of liquid-phase organosilicon precursors, these ceramics offer remarkable engineering properties such as resistance to crystallization up to 1400 °C, semiconductor behavior at high temperatures and intense photoluminescence. These properties are a direct result of their covalent bonded amorphous network and free (-sp2) carbon along with mixed Si/B/C/N/O bonds, which otherwise can not be obtained through conventional ceramic processing techniques. This thesis demonstrates synthesis of a unique core/shell type nanowire structure involving either siliconboroncarbonitride (SiBCN) or siliconoxycarbide (SiOC) as the shell with carbon nanotube (CNT) acting as the core. This was made possible by liquid phase functionalization of CNT surfaces with respective polymeric precursor (e.g., home-made boron-modified polyureamethylvinylsilazane for SiBCN/CNT and commercially obtained polysiloxane for SiOC/CNT), followed by controlled pyrolysis in inert conditions. This unique architecture has several benefits such as high temperature oxidation resistance (provided by the ceramic shell), improved electrical conductivity and mechanical toughness (attributed to the CNT core) that allowed us to explore its use in energy conversion and storage devices. The first application involved use of SiBCN/CNT composite as a high temperature radiation absorbant material for laser thermal calorimeter. SiBCN/CNT spray coatings on copper substrate were exposed to high energy laser beams (continuous wave at 10.6 μm, 2.5 kW CO2 laser, 10 seconds) and resulting change in its microstructure was studied ex-situ. With the aid of multiple techniques we ascertained the thermal damage resistance to be 15 kW/cm2 with optical absorbance exceeding 97 %. This represents one order of magnitude improvement over bare CNTs (1.4 kW/cm2) coatings and two orders of magnitude over the conventional carbon paint (0.1 kW/cm2) currently in use. The second application involved use of SiBCN/CNT and SiOC/CNT composite coatings as energy storage (anode) material in a Li-ion rechargeable battery. Anode coatings (~1mg/cm2) prepared using SiBCN/CNT synthesized at 1100 °C exhibited high reversible (useable) capacity of 412 mAh/g even after 30 cycles. Further improvement in reversible capacity was obtained for SiOC/CNT coatings with 686 mAh/g at 40 cycles and approximately 99.6 % cyclic efficiency. Further, post cycling imaging of dissembled cells indicated good mechanical stability of these anodes and formation of a stable passivating layer necessary for long term cycling of the cell. This improved performance was collectively attributed to the amorphous ceramic shell that offered Li storage sites and the CNT core that provided the required mechanical strength against volume changes associated with repeated Li-cycling. This novel approach for synthesis of PDC nanocomposites and its application based testing offers a starting point to carry out further research with a variety of PDC chemistries at both fundamental and applied levels.

Ce travail de thèse a été consacré au développement d’un système multicouche constitué de nanoparticules dopées par des ions terres rares (le cœur), entourées d’une première couche cristalline non dopée, permettant de préserver les propriétés optiques du cœur. Une coquille de silice mésoporeuse est ensuite déposée, permettant l’incorporation d’un photosensibilisateur (ZnPc) via les pores de la couche de silice pour une application thérapeutique : la photothérapie dynamique. Différentes matrices ont été étudiées à savoir Y2O3, KY3F10 et NaYF4. Ces matrices ont été codopées Yb3+/Er3+ afin d’obtenir des émissions dans le visible sous l’effet d’une excitation infrarouge (upconversion), le but ultime étant d’exciter le ZnPc in situ. Chacune des matrices a été caractérisée d’un point de vue structural et morphologique dans une première partie, et d’un point de vue spectroscopique dans une deuxième partie. La structure cœur-coquille cristalline renforce l’émission rouge issue du niveau 4F9/2 de l’Er, effet déduit de l’analyse des spectres et de la dynamique de luminescence.La détection de l’oxygène singulet a été réalisée par le protocole de « bleaching » en présence ou pas du ZnPc en évaluant l’intensité de fluorescence de l’ABDA. / This work has been dedicated to the development of a multistep system composed by rare earths doped nanoparticles (core), enclosed by a first undoped crystalline layer (core-shell), serving as protection of the optical properties of the core. Within a shell of mesoporous silica allowing the loading of the photosensitizer (ZnPc) via the pores of the shell of silica for a therapeutic application: the photodynamic therapy. Various lattices were studied namely Y2O3, KY3F10 and NaYF4. These lattices were codoped with Yb3+ and Er3+ ions to obtain emissions in the visible under an infrared excitation (up conversion), the ultimate purpose being to excite in situ ZnPc. Each of these lattices was characterized from a structural and morphological point of view in the first part and, in the second part, spectroscopic studies are developed. The core-shell enhances the red emission stemming from the level 4F9/2 of Er, effect deduced from the analysis of spectra and the dynamics of luminescence. The detection of the singlet oxygen was realized in vitro by the study of the bleaching of ABDA fluorescence. The comparison of the results for nanoparticles loaded with ZnPc and unloaded ones allows demonstrating the generation of singlet oxygen by exciting in the infrared region of the spectra thanks to the efficient upconversion processes occurring in the rare earth doped materials.