Small angle scattering characterisation of micellar systems and templated architectures

The work described in this thesis reports the structural changes induced on micelles under a variety of conditions. The micelles of a liquid crystal film and dilute solutions of micelles were subjected to high pressure CO2 and selected hydrocarbon environments. Using small angle neutron scattering (SANS) techniques the spacing between liquid crystal micelles was measured in-situ. The liquid crystals studied were templated from different surfactants with varying structural characteristics. Micelles of a dilute surfactant solution were also subjected to elevated pressures of varying gas atmospheres. Detailed modelling of the in-situ SANS experiments revealed information of the size and shape of the micelles at a number of different pressures. Also reported in this thesis is the characterisation of mesoporous materials in the confined channels of larger porous materials. Periodic mesoporous organosilicas (PMOs) were synthesised within the channels of anodic alumina membranes (AAM) under different conditions, including drying rates and precursor concentrations. In-situ small angle x-ray scattering (SAXS) and transmission electron microscopy (TEM) was used to determine the pore morphology of the PMO within the AAM channels. PMO materials were also used as templates in the deposition of gold nanoparticles and subsequently used in the synthesis of germanium nanostructures. Polymer thin films were also employed as templates for the directed deposition of gold nanoparticles which were again used as seeds for the production of germanium nanostructures. A supercritical CO2 (sc-CO2) technique was successfully used during the production of the germanium nanostructures.

A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

Synthesis of indium nanoparticles at ambient temperature; simultaneous phase transfer and ripening

The synthesis of size-monodispersed indium nanoparticles via an innovative simultaneous phase transfer and ripening method is reported. The formation of nanoparticles occurs in a one-step process instead of well-known two-step phase transfer approaches. The synthesis involves the reduction of InCl3 with LiBH4 at ambient temperature and although the reduction occurs at room temperature, fine indium nanoparticles, with a mean diameter of 6.4 ± 0.4 nm, were obtained directly in non-polar n-dodecane. The direct synthesis of indium nanoparticles in n-dodecane facilitates their fast formation and enhances their size-monodispersity. In addition, the nanoparticles were highly stable for more than 2 months. The nanoparticles were characterised by dynamic light scattering (DLS), small angle X-ray scattering (SAXS), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS) and Fourier transform infrared (FT-IR) spectroscopy to determine their morphology, structure and phase purity.

Dilute nitride semiconductors : band structure, scattering and high field transport

The substitution of a small fraction x of nitrogen atoms, for the group V elements in conventional III-V semiconductors such as GaAs and GaSb strongly perturbs the conduction band of the host semiconductor. In this thesis we investigate the effects of nitrogen states on the band dispersion, carrier scattering and mobility of dilute nitride alloys. In the supercell model we solve the single particle Hamiltonian for a very large supercell containing randomly placed nitrogen. This model predicts a gap in the density of states of GaNxAs1−x, where this gap is filled in the Green’s function model. Therefore we develop a self-consistent Green’s function (SCGF) approach, which provides excellent agreement with supercell calculations and reveals a gap in the DOS, in contrast with the results of previous non-self-consistent Green’s function calculations. However, including the distribution of N states destroys this gap, as seen in experiment. We then examine the high field transport of carriers by solving the steadystate Boltzmann transport equation and find that it is necessary to include the full distribution of N levels in order to account for the small, low-field mobility and the absence of a negative differential velocity regime observed experimentally with increasing x. Overall the results account well for a wide range of experimental data. We also investigate the band structure, scattering and mobility of carriers by finding the poles of the SCGF, which gives lower carrier mobility for GaNxAs1−x, compared to those already calculated, in better agreement with experiments. The calculated optical absorption spectra for InyGa1−yNxAs1−x and GaNxSb1−x using the SCGF agree well with the experimental data, confirming the validity of this approach to study the band structure of these materials.

First-principles calculation of carrier-phonon scattering in n-type Si1−xGex alloys

First-principles electronic structure methods are used to find the rates of inelastic intravalley and intervalley n-type carrier scattering in Si1-xGex alloys. Scattering parameters for all relevant Delta and L intra- and intervalley scattering are calculated. The short-wavelength acoustic and the optical phonon modes in the alloy are computed using the random mass approximation, with interatomic forces calculated in the virtual crystal approximation using density functional perturbation theory. Optical phonon and intervalley scattering matrix elements are calculated from these modes of the disordered alloy. It is found that alloy disorder has only a small effect on the overall inelastic intervalley scattering rate at room temperature. Intravalley acoustic scattering rates are calculated within the deformation potential approximation. The acoustic deformation potentials are found directly and the range of validity of the deformation potential approximation verified in long-wavelength frozen phonon calculations. Details of the calculation of elastic alloy scattering rates presented in an earlier paper are also given. Elastic alloy disorder scattering is found to dominate over inelastic scattering, except for almost pure silicon (x approximate to 0) or almost pure germanium (x approximate to 1), where acoustic phonon scattering is predominant. The n-type carrier mobility, calculated from the total (elastic plus inelastic) scattering rate, using the Boltzmann transport equation in the relaxation time approximation, is in excellent agreement with experiments on bulk, unstrained alloys..