G-quadruplex forming human telomere sequence (HTS) DNA, has been widely studied due to the telomere's implied role in biological processes, including cellular ageing and cancer physiology. The goal of these previous efforts has been to characterize the physiologically relevant structures and their stability and dynamics in order to develop therapeutic applications. Unfortunately, understanding the biologically relevant form of the human telomere DNA is complicated by the fact that HTS-derived sequences are highly polymorphic. To further complicate the issue, recent investigations have demonstrated the ability of "cell-like" co-solvents to alter the preferred G-quadruplex fold of HTS DNA. However, the origins of G-quadruplex structure selection, the relative contributions of crowding versus dehydration, and the possible effects of co-solvents on kinetically determined folding pathways remain unresolved. Towards answering these questions, I investigated HTS DNA G-quadruplex in extreme anhydrous and high viscosity conditions utilizing a deep eutectic solvent (DES) consisting of choline chloride and urea. Herein I report that the water-free DES supports an extremely stable parallel stranded structure, consistent with observations that diminished water activity is the main cause of structural transitions to the "parallel-propeller" form. Furthermore, my research shows that the highly viscous nature of the solvent enables significant diffusion based control over HTS g-quadruplex folding rates and topology, fully consistent with Kramers rate theory. To the best of my knowledge, this is the first example of the kinetic exploration of G-quadruplex folding utilizing high friction solvent; the results of which display a decreased intramolecular folding rate of HTS DNA to a never before encountered time scale on the order of days at physiological temperature. Moreover, I have demonstrated that the folding pathway of a G-quadruplex can be altered with increased solvent friction. These discoveries are important because they highlight the need to consider the viscosity when exploring the dynamics of human telomeres specifically drug binding and folding of G-quadruplexes in vivo where cellular viscosity has been reported to be as high as 140cP. Lastly, it appears that tuning solvent viscosity could prove useful to the continued study of G-quadruplex dynamics.

Photopolymerization is the basis of several multi-million dollar industries including films and coating, inks, adhesives, fiber optics, and biomaterials. The fundamentals of the photopolymerization process, however, are not well understood. As a result, spatial variations of photopolymerization impose significant limitations on applications in which a high spatial resolution is required. To address these issues, microrheology was implemented to study the spatial and temporal effects of free-radical photopolymerization. In this work a photosensitive, acrylate resin was exposed to ultraviolet light, while the Brownian motion of micron sized, inert fluorescent tracer particles was tracked using optical videomicroscopy. Statistical analysis of particle motion yielded data that could then be used to extract rheological information about the embedding medium as a function of time and space, thereby relating UV exposure to the polymerization and gelation of monomeric resins. The effects of varying depth, initiator concentration, inhibitor concentration, composition of the monomer, and light intensity on the gelation process were studied. The most striking result is the measured difference in gelation time observed as a function of UV penetration depth. The observed trend was found to be independent of UV light intensity and monomer composition. The intensity results were used to test the accuracy of energy threshold model, which is used to empirically predict photo-induced polymerization. The results of this research affirm the ability of microrheology to provide the high spatial and temporal resolution necessary to accurately monitor the photopolymerization process. The experimental data provide a better understanding of the photo-induced polymerization, which could lead to expanded use and improved industrial process optimization. The use of microrheology to monitor photopolymerization can also aid in the development of predictive models and offer the ability to perform in-situ quality control of the process.

Nanoalloys are an exciting new class of materials in the growing field of nanotechnology. Nanoalloys consist of the nanoscale co-aggregation of two or more metals with a potential to form compositionally-ordered phases or superstructures that have properties unlike those of the individual metal clusters or of bulk alloys of the constituent metals. This research seizes the opportunity that the nanoscale domain has to offer, and focuses on the synthesis of iron and cobalt nanoalloys via the simultaneous decomposition of iron cobalt organometallic precursors in a stabilizing environment, accompanied by the thorough characterization of the resulting nanoclusters. Zero-valent FeCo nanoalloys may potentially have interesting uses as magnetic materials. Since these clusters have sizes less than the size of their magnetic domain, the clusters will exhibit single domain magnetism. This magnetism may be observed by the presence of chain structures of FeCo nanoclusters due to the alignment of their single magnetic domains. In order to create a near-atomically homogeneous nanoalloy without preferential aggregation of its metal atom constituents, no clustering and phase separation should take place. In the bulk, alloys of iron and cobalt phase separate over most of the compositional range. Conversely, at the nanoscale, it may be possible to synthesize nanoalloy structures that are not normally favorable at given compositions, by the manipulation of reaction kinetics. In order to produce an atomically mixed nanoalloy, the transformation reactions of the organometallic precursors should display similar kinetic features, i.e. similar reaction rates. Therefore, the reaction kinetics of all the species in the reaction must be similar to avoid competition between them. As a result, kinetic control of the individual transformation reaction rates of each species may be used to modulate the aggregation and phase separation of the different species, and consequently control cluster morphology. This work has provided the framework for the design of synthesis methods that enable the control of the structure of FeCo nanoalloys with careful attention to precursor decomposition kinetics and the correlation between reaction kinetics and nanoalloy morphology.

Two new models to calculate the species instantaneous and filtered reaction rates for multi-step, multi-species chemical kinetics mechanisms are developed based on the artificial neural networks (ANN) approach. The proposed methodologies depend on training the ANNs off-line on a thermo-chemical database representative of the actual composition and turbulence level of interest. The thermo-chemical database is constructed by stand-alone linear eddy mixing (LEM) model simulations under both premixed and non-premixed conditions, where the unsteady interaction of turbulence with chemical kinetics is included as a part of the training database. In this approach, the information regarding the actual geometry of interest is not needed within the LEM computations. The developed models are validated extensively on the large eddy simulations (LES) of (i) premixed laminar-flame-vortex-turbulence interaction, (ii) temporally mixing non-premixed flame with extinction-reignition characteristics, and (iii) stagnation point reverse flow combustor, which utilizes exhaust gas re-circulation technique. Results in general are satisfactory, and it is shown that the ANN provides considerable amount of memory saving and speed-up with reasonable and reliable accuracy. The speed-up is strongly affected by the stiffness of the reduced mechanism used for the computations, whereas the memory saving is considerable regardless.

Gas-expanded liquids (GXLs) are a unique class of tunable solvents with unlimited potential. A wide range of solvent properties and solvent interactions and complexes are possible by adjusting the amount of the gas component (in situ) or changing the organic liquid. Aside from solvent tunability, there are environmental and processing benefits to using GXLs. Organic solvent use is decreased, the gas component can be vented off facile separations, and the gas can act as an antisolvent for selective solute precipitation. As a result there are numerous reaction and extraction schemes and materials processing applications that could benefit from GXL use. Unfortunately, important molecular-level details that can drive a chemical process are largely unknown and limit GXL use in industrial and specialty applications. The work presented in this uses a synergistic study of experiments and computer simulations to explore solvation processes and molecular interactions in GXLs and the effects on macroscopic observables like spectroscopy, transport, and reactions. Steady-state solvation of a laser dye is studied with spectroscopy (UV/vis and fluorescence) and molecular dynamics simulations (MD). Both experiment and theory show that organic enrichment occurs in the vicinity of the solute called the cybotactic region. Subsequently, the solvent dynamics arising by electronically perturbing the solute are studied with MD simulation. Unexpected dynamics are observed and are dependent on the organic component and gas composition. The diffusion of heterocyclic compounds is studied with MD simulations and compared to the Taylor-Aris diffusion study of former group members. The experiments and simulations do not agree, but solvent structures obtained by simulation are shown to provide valuable insight into solvent-dependent absorption spectroscopy, or solvatochromism. Finally, dissociation constants of alkylcarbonic acids that form in situ in CO2/alcohol mixtures are presented from spectroscopic measurements. Spectroscopic techniques to measure dissociation constants are well known; however, the high-pressure and multiple equilibria associated with alkylcarbonic acids hinder straight-forward measurement and analysis.

A number of weakly bound adducts play important roles in atmospheric chemistry, such as DMS OH and CS2 OH. The work comprising this dissertation involves kinetic and spectroscopic studies of adducts formed between halogen atoms and the important atmospheric trace gases CS2, CH3SCH3 (DMS), CH3I, and C2H5I. The results reported in these studies are useful for developing an understanding of the reactivity of these species and for testing the ability of electronic structure theory and reaction rate theory to predict or rationalize any observed trends. Oxidative pathways of both alkyl halides and sulfur compounds, especially DMS, are of atmospheric interest based on the roles of these species in affecting the oxidizing capacity of the troposphere and in the formation of new particles which impact the Earth s radiation budget and climate variability. The experimental approach employed laser flash photolysis (LFP) coupled with time resolved UV-visible absorption spectroscopy (TRUVVAS) to investigate the spectroscopy and kinetics of the gas phase adducts: SCS Cl, CH3I Cl, C2H5I Cl, (CH3)2S Br, and (CH3)2S I.

Irradiation with ultraviolet (UV) light is used for the disinfection of bacterial contaminants in the production of potable water, and in the treatment of selected wastewaters. However, efficacy of UV disinfection is limited by the combined effect of suspended solids concentration and UV absorbance. Limited published UV disinfection data are available that account for the combined effects of UV dose, suspended solids concentration and UV absorbance. This present lack of a rigorous quantitative understanding of the kinetics of UV disinfection limits process optimisation and wider application of UV treatment. The development and validation of an adequate model to describe UV disinfection kinetics presented in this thesis can therefore be justified by an increased confidence of reliability of design for UV disinfection. Using the published data of Nguyen (1999), four established model forms were assessed to account for the combined effect of suspended solids and/or soluble UV absorbing compounds, and UV dose on the efficacy of disinfection. The four model forms were: a log-linear form, Davey Linear-Arrhenius (DL-A), Square-Root (or Ratkowsky- Belehradek) and a general nth order Polynomial (nOP) form that was limited to a third order. Criteria for assessment of an adequate predictive model were established including: accuracy of predicted against observed values, percent variance accounted for (%V), and; appraisal of residuals. The DL-A model was shown to best fit the data for UV disinfection of Escherichia coli (ATCC 25922); followed by the nOP, log-linear and Square-Root forms. However, the DL-A form must be used in conjunction with a first-order chemical reaction equation, and was shown to predict poorly at high experimental values of UV dose (> 40,000 μWs cm-2). The DL-A model was not amenable to extrapolation beyond the observed UV dose range. To overcome the shortcomings of the Davey Linear-Arrhenius model synthesis of two new, non-linear model forms was undertaken. The two models were a modified exponentially damped polynomial (EDPm) and a form based on the Weibull probability distribution. The EDPm model has three terms: a rate coefficient (k), a damping coefficient (λ), and; a breakpoint dose ([dose]B). The rate coefficient governs the initial rate of disinfection prior to the onset of tailing, whilst the breakpoint is the UV dose that indicates the onset of tailing. The damping coefficient controls curvature in the survivor curve. The Weibull model has just two terms: a dimensionless scale parameter (β0), and; a shape parameter (β1). The scale parameter represents the level of disinfection in the tail of the survivor curve (as log10 N/N0), whilst the shape parameter governs the degree of curvature of the survivor data. Each model was assessed against the independent and published UV disinfection data of Nelson (2000) for treatment of faecal coliforms in a range of waste stabilisation pond effluents. Both models were found to be well suited to account for tailing in these UV disinfection data. Overall, the EDPm model gave a better fit to the data than the Weibull model form. To rigorously validate the suitability of the new EDPm and Weibull models a series of experimental trials were designed and carried out in a small-scale pilot UV disinfection unit. These trials included data determined specifically at low values of UV dose (<10,000 μWs cm-2) to fill the gap in the experimental data of Nguyen (1999). The experimental trials were carried out using a commercially available, UV disinfection unit (LC5TM from Ultraviolet Technology of Australasia Pty Ltd). Purified water contaminated with Escherichia coli (ATCC 25922) with a range of feed water flow rates (1 to 4 L min-1) was used. E. coli was selected because it is found in sewage, or water contaminated with faecal material, and is used as an indicator for the presence of enteric pathogens. E. coli should not be present in potable water. The hydrodynamics of water flow within the disinfection unit were established using digital video photography of dye trace studies with Methylene Blue. Nominal UV dose (2,700 to 44,200 μWs cm-2) was controlled by manipulating the flow rate of feed water through the UV disinfection unit (i.e. residence time), or by varying the exposed length of the control volume of the disinfection unit. The transmittance of the feed water (at 254 nm) was adjusted by the addition of either a soluble UV absorbing agent (International RoastTM instant coffee powder; 0.001 to 0.07 g L-1), or by addition of suspended matter as diatomaceous earth (Celite 503TM; 0.1 to 0.7 g L-1, with a median particle size of 23 μm). The absorbing agent (instant coffee), when in a comparable concentration, was found to produce a greater reduction in water transmission than the suspended material (Celite 503TM). It therefore contributed to a greater reduction in the initial rate of disinfection. Neither agent was found to produce a systematic reduction in the observed efficacy of disinfection however. Experimental results highlight that in the absence of soluble absorbing agents, or suspended solids, the initial rate of disinfection is higher when fewer viable bacteria are initially present. Both the new EDPm and Weibull forms gave a good fit to the experimental data. The EDPm better fitted the data on the basis of residual sum-of-squares (0.03 to 2.13 for EDPm cf. 0.16 to 4.37 for the Weibull form). These models are both of a form suitable for practical use in modelling UV disinfection data. Results of this research highlight the impact of water quality, as influenced by the combined effect of UV dose, suspended solids concentration and UV absorbance, on small-scale UV disinfection for potable water production. Importantly, results show that the concentration of soluble UV absorbing agents and suspended solids are not in themselves sufficient criteria on which to base assessment of efficacy of UV disinfection / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1342403 / Thesis (M.Eng.Sc.) - University of Adelaide, School of Chemical Engineering, 2008

Irradiation with ultraviolet (UV) light is used for the disinfection of bacterial contaminants in the production of potable water, and in the treatment of selected wastewaters. However, efficacy of UV disinfection is limited by the combined effect of suspended solids concentration and UV absorbance. Limited published UV disinfection data are available that account for the combined effects of UV dose, suspended solids concentration and UV absorbance. This present lack of a rigorous quantitative understanding of the kinetics of UV disinfection limits process optimisation and wider application of UV treatment. The development and validation of an adequate model to describe UV disinfection kinetics presented in this thesis can therefore be justified by an increased confidence of reliability of design for UV disinfection. Using the published data of Nguyen (1999), four established model forms were assessed to account for the combined effect of suspended solids and/or soluble UV absorbing compounds, and UV dose on the efficacy of disinfection. The four model forms were: a log-linear form, Davey Linear-Arrhenius (DL-A), Square-Root (or Ratkowsky- Belehradek) and a general nth order Polynomial (nOP) form that was limited to a third order. Criteria for assessment of an adequate predictive model were established including: accuracy of predicted against observed values, percent variance accounted for (%V), and; appraisal of residuals. The DL-A model was shown to best fit the data for UV disinfection of Escherichia coli (ATCC 25922); followed by the nOP, log-linear and Square-Root forms. However, the DL-A form must be used in conjunction with a first-order chemical reaction equation, and was shown to predict poorly at high experimental values of UV dose (> 40,000 μWs cm-2). The DL-A model was not amenable to extrapolation beyond the observed UV dose range. To overcome the shortcomings of the Davey Linear-Arrhenius model synthesis of two new, non-linear model forms was undertaken. The two models were a modified exponentially damped polynomial (EDPm) and a form based on the Weibull probability distribution. The EDPm model has three terms: a rate coefficient (k), a damping coefficient (λ), and; a breakpoint dose ([dose]B). The rate coefficient governs the initial rate of disinfection prior to the onset of tailing, whilst the breakpoint is the UV dose that indicates the onset of tailing. The damping coefficient controls curvature in the survivor curve. The Weibull model has just two terms: a dimensionless scale parameter (β0), and; a shape parameter (β1). The scale parameter represents the level of disinfection in the tail of the survivor curve (as log10 N/N0), whilst the shape parameter governs the degree of curvature of the survivor data. Each model was assessed against the independent and published UV disinfection data of Nelson (2000) for treatment of faecal coliforms in a range of waste stabilisation pond effluents. Both models were found to be well suited to account for tailing in these UV disinfection data. Overall, the EDPm model gave a better fit to the data than the Weibull model form. To rigorously validate the suitability of the new EDPm and Weibull models a series of experimental trials were designed and carried out in a small-scale pilot UV disinfection unit. These trials included data determined specifically at low values of UV dose (<10,000 μWs cm-2) to fill the gap in the experimental data of Nguyen (1999). The experimental trials were carried out using a commercially available, UV disinfection unit (LC5TM from Ultraviolet Technology of Australasia Pty Ltd). Purified water contaminated with Escherichia coli (ATCC 25922) with a range of feed water flow rates (1 to 4 L min-1) was used. E. coli was selected because it is found in sewage, or water contaminated with faecal material, and is used as an indicator for the presence of enteric pathogens. E. coli should not be present in potable water. The hydrodynamics of water flow within the disinfection unit were established using digital video photography of dye trace studies with Methylene Blue. Nominal UV dose (2,700 to 44,200 μWs cm-2) was controlled by manipulating the flow rate of feed water through the UV disinfection unit (i.e. residence time), or by varying the exposed length of the control volume of the disinfection unit. The transmittance of the feed water (at 254 nm) was adjusted by the addition of either a soluble UV absorbing agent (International RoastTM instant coffee powder; 0.001 to 0.07 g L-1), or by addition of suspended matter as diatomaceous earth (Celite 503TM; 0.1 to 0.7 g L-1, with a median particle size of 23 μm). The absorbing agent (instant coffee), when in a comparable concentration, was found to produce a greater reduction in water transmission than the suspended material (Celite 503TM). It therefore contributed to a greater reduction in the initial rate of disinfection. Neither agent was found to produce a systematic reduction in the observed efficacy of disinfection however. Experimental results highlight that in the absence of soluble absorbing agents, or suspended solids, the initial rate of disinfection is higher when fewer viable bacteria are initially present. Both the new EDPm and Weibull forms gave a good fit to the experimental data. The EDPm better fitted the data on the basis of residual sum-of-squares (0.03 to 2.13 for EDPm cf. 0.16 to 4.37 for the Weibull form). These models are both of a form suitable for practical use in modelling UV disinfection data. Results of this research highlight the impact of water quality, as influenced by the combined effect of UV dose, suspended solids concentration and UV absorbance, on small-scale UV disinfection for potable water production. Importantly, results show that the concentration of soluble UV absorbing agents and suspended solids are not in themselves sufficient criteria on which to base assessment of efficacy of UV disinfection / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1342403 / Thesis (M.Eng.Sc.) - University of Adelaide, School of Chemical Engineering, 2008

Irradiation with ultraviolet (UV) light is used for the disinfection of bacterial contaminants in the production of potable water, and in the treatment of selected wastewaters. However, efficacy of UV disinfection is limited by the combined effect of suspended solids concentration and UV absorbance. Limited published UV disinfection data are available that account for the combined effects of UV dose, suspended solids concentration and UV absorbance. This present lack of a rigorous quantitative understanding of the kinetics of UV disinfection limits process optimisation and wider application of UV treatment. The development and validation of an adequate model to describe UV disinfection kinetics presented in this thesis can therefore be justified by an increased confidence of reliability of design for UV disinfection. Using the published data of Nguyen (1999), four established model forms were assessed to account for the combined effect of suspended solids and/or soluble UV absorbing compounds, and UV dose on the efficacy of disinfection. The four model forms were: a log-linear form, Davey Linear-Arrhenius (DL-A), Square-Root (or Ratkowsky- Belehradek) and a general nth order Polynomial (nOP) form that was limited to a third order. Criteria for assessment of an adequate predictive model were established including: accuracy of predicted against observed values, percent variance accounted for (%V), and; appraisal of residuals. The DL-A model was shown to best fit the data for UV disinfection of Escherichia coli (ATCC 25922); followed by the nOP, log-linear and Square-Root forms. However, the DL-A form must be used in conjunction with a first-order chemical reaction equation, and was shown to predict poorly at high experimental values of UV dose (> 40,000 μWs cm-2). The DL-A model was not amenable to extrapolation beyond the observed UV dose range. To overcome the shortcomings of the Davey Linear-Arrhenius model synthesis of two new, non-linear model forms was undertaken. The two models were a modified exponentially damped polynomial (EDPm) and a form based on the Weibull probability distribution. The EDPm model has three terms: a rate coefficient (k), a damping coefficient (λ), and; a breakpoint dose ([dose]B). The rate coefficient governs the initial rate of disinfection prior to the onset of tailing, whilst the breakpoint is the UV dose that indicates the onset of tailing. The damping coefficient controls curvature in the survivor curve. The Weibull model has just two terms: a dimensionless scale parameter (β0), and; a shape parameter (β1). The scale parameter represents the level of disinfection in the tail of the survivor curve (as log10 N/N0), whilst the shape parameter governs the degree of curvature of the survivor data. Each model was assessed against the independent and published UV disinfection data of Nelson (2000) for treatment of faecal coliforms in a range of waste stabilisation pond effluents. Both models were found to be well suited to account for tailing in these UV disinfection data. Overall, the EDPm model gave a better fit to the data than the Weibull model form. To rigorously validate the suitability of the new EDPm and Weibull models a series of experimental trials were designed and carried out in a small-scale pilot UV disinfection unit. These trials included data determined specifically at low values of UV dose (<10,000 μWs cm-2) to fill the gap in the experimental data of Nguyen (1999). The experimental trials were carried out using a commercially available, UV disinfection unit (LC5TM from Ultraviolet Technology of Australasia Pty Ltd). Purified water contaminated with Escherichia coli (ATCC 25922) with a range of feed water flow rates (1 to 4 L min-1) was used. E. coli was selected because it is found in sewage, or water contaminated with faecal material, and is used as an indicator for the presence of enteric pathogens. E. coli should not be present in potable water. The hydrodynamics of water flow within the disinfection unit were established using digital video photography of dye trace studies with Methylene Blue. Nominal UV dose (2,700 to 44,200 μWs cm-2) was controlled by manipulating the flow rate of feed water through the UV disinfection unit (i.e. residence time), or by varying the exposed length of the control volume of the disinfection unit. The transmittance of the feed water (at 254 nm) was adjusted by the addition of either a soluble UV absorbing agent (International RoastTM instant coffee powder; 0.001 to 0.07 g L-1), or by addition of suspended matter as diatomaceous earth (Celite 503TM; 0.1 to 0.7 g L-1, with a median particle size of 23 μm). The absorbing agent (instant coffee), when in a comparable concentration, was found to produce a greater reduction in water transmission than the suspended material (Celite 503TM). It therefore contributed to a greater reduction in the initial rate of disinfection. Neither agent was found to produce a systematic reduction in the observed efficacy of disinfection however. Experimental results highlight that in the absence of soluble absorbing agents, or suspended solids, the initial rate of disinfection is higher when fewer viable bacteria are initially present. Both the new EDPm and Weibull forms gave a good fit to the experimental data. The EDPm better fitted the data on the basis of residual sum-of-squares (0.03 to 2.13 for EDPm cf. 0.16 to 4.37 for the Weibull form). These models are both of a form suitable for practical use in modelling UV disinfection data. Results of this research highlight the impact of water quality, as influenced by the combined effect of UV dose, suspended solids concentration and UV absorbance, on small-scale UV disinfection for potable water production. Importantly, results show that the concentration of soluble UV absorbing agents and suspended solids are not in themselves sufficient criteria on which to base assessment of efficacy of UV disinfection / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1342403 / Thesis (M.Eng.Sc.) - University of Adelaide, School of Chemical Engineering, 2008

Thesis (Ph.D. (Chemistry)) - Rhodes University, 2008.