Please read the abstract in the section 00front of this document / Dissertation (MSc (Applied Sciences:Chemistry))--University of Pretoria, 2005. / Chemistry / unrestricted

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Time-Resolved diffuse optics is a powerful and safe technique to quantify the optical properties (OP) for highly scattering media such as biological tissues. The OP values are correlated with the compositions of the measured objects, especially for the tissue chromophores such as hemoglobin. The OP are mainly the absorption and the reduced scattering coefficients that can be quantified for highly scattering media using Time-Resolved Diffuse Optical Spectroscopy (TR-DOS) systems. The OP can be retrieved using Time-Resolved Diffuse Optical Imaging (TR-DOI) systems to reconstruct the distribution of the OP in measured media. Therefore, TR-DOS and TR-DOI can be used for functional monitoring of brain and muscles, and to diagnose some diseases such as detection and localization for breast cancer and blood clot. In general, TR-DOI systems are non-invasive, reliable, and have a high temporal resolution. TR-DOI systems have been known for their complexity, bulkiness, and costly equipment such as light sources (picosecond pulsed laser) and detectors (single photon counters). Also, TR-DOI systems acquire a large amount of data and suffer from the computational cost of the image reconstruction process. These limitations hinder the usage of TR-DOI for widespread potential applications such as clinical measurements. The goals of this research project are to investigate approaches to eliminate two main limitations of TR-DOI systems. First, building TR-DOS systems using custom-designed free-running (FR) and time-gated (TG) SPAD detectors that are fabricated in low-cost standard CMOS technology instead of the costly photon counting and timing detectors. The FR-TR-DOS prototype has demonstrated comparable performance (for homogeneous objects measurements) with the reported TR-DOS prototypes that use commercial and expensive detectors. The TG-TR-DOS prototype has acquired raw data with a low level of noise and high dynamic range that enable this prototype to measure multilayered objects such as human heads. Second, building and evaluating TR-DOI prototype that uses a computationally efficient algorithm to reconstruct high quality 3D tomographic images by analyzing a small part of the acquired data. This work indicates the possibility to exploit the recent advances in the technologies of silicon detectors, and computation to build low-cost, compact, portable TR-DOI systems. These systems can expand the applications of TR-DOI and TR-DOS into several fields such as oncology, and neurology. / Thesis / Doctor of Philosophy (PhD)

This thesis describes and develops two experimental techniques, Time Resolved Photoelectron Spectroscopy (TRPES), and Time Resolved Coincidence Imaging Spectroscopy (TRCIS), to study ultrafast gas phase chemical dynamics. We use TRPES to investigate the effects of methyl substitution on the electronic dynamics of the simple alpha, beta-enones acrolein, crotonaldehyde, methylvinylketone, and methacrolein following excitation to the S2 state. We determine that following excitation, the molecules move rapidly away from the Franck-Condon region reaching a conical intersection promoting relaxation to the S1 state. Once on the S1 surface, the trajectories access another conical intersection leading them to the ground state. Only small variations between molecules are seen in their S2 decay times. However, the position of methyl group substitution greatly affects the relaxation rate from the S1 surface. Ab initio calculations used to compare the geometries, energies, and topographies of the S1/S0 conical intersections of the molecules are not able to explain the variations in relaxation behaviour. We propose a model that uses dynamical factors of specific motions in the molecules to explain the differing nonadiabatic S1/S0 crossing rates. The second part of this thesis examines the issues involved with design and construction of a Coincidence Imaging Spectrometer. This type of spectrometer measures the 3-dimensional velocities of both photoelectrons and photoions generated from probing of laser induced photodissociation reactions. Importantly, the photoelectrons and photoions are measured in coincidence from single molecules, enabling measurements such as recoil frame photoelectron angular distributions and correlated photoelectron/photoion energy maps, inaccessible using existing techniques. How to optimize the spectrometer resolution through design, tuning, and calibration is discussed. The power of TRCIS is demonstrated with the investigation of the photodissociation dynamics of the NO dimer. TRPES experiments first identified a sequential kinetic model following 209nm excitation resulting in NO(X) (ground state) and NO(A) (excited state) products. Using TRCIS, it was possible to measure time resolved vibrational energy distributions of the products, indicating the extent of vibrational energy redistribution within the dimers prior to dissociation. Recoil frame photoelectron angular distributions and theoretical support allow identification of a previously disputed intermediate on the dissociation pathway. / Thesis (Ph.D, Chemistry) -- Queen's University, 2007-04-01 10:12:39.968

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published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Restriction modification (RM) systems play a crucial role in preventing the entry of foreign DNA into the bacterial cell. The best studied Type I RM system is EcoKI from Escherichia coli K12. Both bacteriophage and conjugative plasmids have developed a variety of strategies to circumvent the host RM system. One such strategy involves the production of antirestriction proteins that mimic a short segment of DNA and efficiently inhibit the RM system. The main aim of this project was to analyse the interaction of EcoKI and its cognate methylase (MTase) with the T7 antirestriction protein, known as overcome classical restriction (Ocr), and various ArdA antirestriction proteins. Currently, there is a paucity of structural data on the complex formed between the Type I system and the antirestriction proteins. The aim of this work was twofold; (i) compare the interaction of MTase with DNA and Ocr and (ii) quantify the strength of interaction between MTase and various ArdA proteins. The MTase was fused to the Green Fluorescent Protein (GFP) to facilitate determination of the orientation of interaction with DNA and Ocr. Time resolved fluorescence measurements were carried out using the GFP-MTase fusion to determine the fluorescence lifetime and anisotropy decay. These experiments were conducted using a time resolved fluorescence instrument fabricated in-house. The values determined in these experiments were then used to perform fluorescence resonance energy transfer (FRET) measurements with fluorescently labelled DNA or Ocr. These measurements gave information concerning the relative orientation of the MTase with either DNA or Ocr. The GFP-MTase fusion was also used to quantify the strength of interaction with various ArdA proteins. Previous attempts to determine the strength of interaction between MTase and ArdA proteins by employing conventional techniques have been unsuccessful. Therefore, a novel method was developed that exploits the interaction of MTase with a cation exchange medium, which can subsequently be displaced upon binding to ArdA. This method facilitated the determination, for the first time, of a set of binding affinities for the MTase and ArdA interaction.

Since its inception a quarter of a century ago, Kelvin probe force microscopy (KPFM) has enabled studying contact potential differences (CPDs) on the nanometre scale. However, current KPFM investigations are limited by the bandwidth of its constituent electronic loops to the millisecond regime. To overcome this limitation, pump-probe-driven Kelvin probe force microscopy (pp-KPFM) is introduced that exploits the non-linear electric interaction between tip and sample. The time resolution surpasses the electronic bandwidth and is limited by the length of the probe pulse. In this work, probe pulse lengths as small as 4.5 ns have been realized. These probe pulses can be synchronized to any kind of pump pulses. The first system investigated with pp-KPFM is an electrically-driven organic field-effect transistor (OFET). Here, charge carrier propagation in the OFET channel upon switching the drain-source voltage is directly observed and compared to simulations based on a transmission line model. Varying the charge carrier density reveals the impeding influence of Schottky barriers on the maximum switching frequency. The second system is an optically-modulated silicon homojunction. Here, the speed of surface photovoltage (SPV) build-up is accessed and compared to timeaveraged results. Due to slow trap states, the time-averaged method is found to lack comprehensiveness. In contrast, pp-KPFM exposes two intensity-dependent recombination times on the same timescale — high-level Shockley-Read-Hall recombination in the bulk and heat-dominated recombination in the surface layer — and a delay of the SPV decay with rising frequency, which is attributed to charge carrier retention at nanocrystals. The third system is a DCV5T-Me:C60 bulk heterojunction. The SPV dynamics is probed and compared to measurements via open-circuit corrected transient charge carrier extraction by linearly increasing voltage. Both methods reveal an exponential onset of the band bending reduction that is attributed to the charge carrier diffusion time in DCV5T-Me, and a double exponential decay, hinting at different recombination paths in the studied organic solar cell. The above-mentioned experiments demonstrate that pp-KPFM surpasses conventional KPFM when it comes to extracting dynamic device parameters such as charge carrier retention and recombination times, and prove that pp-KPFM is a versatile and reliable tool for studying electrodynamics on nanosurfaces.