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Thesis (Ph.D.)-University of Natal, Durban, 1987.

Threefoil is a small engineered protein of 141 amino acids which is a member of the beta-trefoil superfamily, with three-fold symmetry and high thermal and kinetic stability. Its primary sequence was designed based on a predicted beta-trefoil glycosidase from the halophilic Archaeon Haloarcula marismortui. Threefoil predominantly forms inclusion bodies when over-expressed in Escherichia coli at 37??C, with little to no protein soluble in the cytoplasm. Nevertheless, Threefoil is capable of adopting a native beta-trefoil structure when refolded from solubilized inclusion bodies. The focus of this thesis is on characterization of the folding and stability of Threefoil through thermodynamic and kinetic experiments for wild-type Threefoil, in addition to sugar- and metal-binding studies and characterization of Threefoil inclusion bodies. Various Threefoil mutants, designed to increase protein stability, are also characterized to probe the origins of, as well as to give insight into, the mechanism of inclusion body formation. The thermodynamic and kinetic stability of wild-type Threefoil was studied using spectral probes, mainly fluorescence, circular dichroism (CD) and dynamic light scattering (DLS). The major observed spectral changes in kinetic and thermodynamic experiments can be fit to a 2-state transition between the folded state and a denatured state containing extensive residual secondary structure. At high protein concentrations, the folding of wild-type Threefoil is complicated by protein misfolding and aggregation. As Threefoil is remarkably resistant to denaturation even at high concentrations of urea and guanidine hydrochloride (GuHCl), studies were also conducted in guanidine isothiocyanate (GuSCN), which is a much stronger denaturant than urea and GuHCl. Remarkably, the time that is required for Threefoil samples to reach equilibrium in renaturation curves is approximately 100 days, while equilibrium by denaturation in the stronger denaturant, GuSCN, requires more than two years. The expression levels of Threefoil mutants A62V, Q78I, D85P and D93P were also studied. None of the four mutants studied exhibited any pronounced increase in solubility compared to wild-type when expressed in E. coli.

There has been an increasing focus on using nanoscale devices for various applications ranging from computer components to biomechanical sensors. In order to effectively design devices of this size, it is important to understand the properties of materials at this length scale and their relevant transport equations. At everyday length scales, heat transport is governed by Fourier’s law, but at the nanoscale, it becomes increasingly inaccurate. Phonon kinetic theory can be used to develop more accurate governing equations. We present the moment method, which takes integral moments of the phonon Boltzmann kinetic equation to develop a set of equations based on macroscopic properties such as energy and heat flux. The advantage of using this method is that transport properties in nanodevices can be approximated analytically and efficiently. A number of simplifying assumptions are used in order to linearize the equations. Boundary conditions for the moment method are derived based on a microscopic model of phonons interacting with a surface by scattering, reflection or thermalization. Several simple, one dimensional problems are solved using the moment method equation. The results show the effects of phonon surface interactions and how they affect overal properties of a nanoscale device. Some of these effects were observed in a recent experiment and are replicated by other modeling techniques. Although the moment method has described some effects of nanoscale heat transfer, the model is limited by some of its simplifying assumptions. Several of these simplifying assumptions could be removed for greater accuracy, but it would introduce non-linearity into the moment method. / Graduate

We have developed novel experiments aimed at understanding whether and how quickly organic aerosols (OA) mix using single-particle mass spectrometry, as different treatments of mixing in regional models significantly affect predicted mass and composition. First, we designed experiments that separate OA formation chemistry from thermodynamics to test whether two populations of particles equilibrate with eachother through the gas phase on experimental timescales. Single-particle mass spectrometry measurements from the aerosol mass spectrometer (AMS) allowed us to quantify the extent of mixing that had occurred. We calibrated this technique using pure-component aerosols with known vapor pressure and phase state, the results of which agreed with a condensation-evaporation model. We then applied these techniques to three atmospherically-relevant situations to determine that: 1) anthropogenic secondary OA (aSOA) does not mix with a surrogate for hydrophobic primary OA (POA), 2) biogenic SOA (bSOA) does not mix with hydophobic POA, and 3) bSOA shows significant mixing with aSOA. The sum of these experiments show that these complex interactions can be measured for atmospherically important systems, a first step towards quantifying activity coefficients for complex OA mixtures. We also investigated mixing within individual particles, using mixed-particles of squalane (a surrogate for hydrophobic POA) and SOA from ↵+pinene + O3 that we determined to contain two separate phases. In these experiments, after formation of the mixed-particles, we perturbed smog chamber with a heat ramp. These data revealed that squalane is able to quickly evaporate from the mixed-particles, and that almost all of the SOA is comprised of material lower in volatility than squalane (a low-volatility constituent of pump oil). For this latter “comparative volatility analysis,” we had to correct for the highly variable collection efficiency (CE) of the mixed particles to correctly calculate the mass fraction of SOA remaining. One of the larger implications of this work is highly dependent on the particle morphology, which we were not able to determine definitively: if indeed the particles are coreshell with squalane inside a thick layer of SOA, our results show that diffusivity within SOA is not ultra-low. Lastly, we present work that furthers our understanding of single-particle CE in the AMS, a quantity especially important for experiments where particle phase is dynamic or there are two separate populations of particles. We report the particle CE of SOA, ammonium sulfate, ammonium nitrate, and squalane. We also determine that half of SOA particles that give meaningful signal, do so at a time later than would be predicted based on their optically-measured flight time through the instrument. We present convincing evidence that the nature of this delay is due to particles ricocheting around the ionization region of the instrument before vaporizing on an auxillary surface near the the vaporizer. This process affects how much mass signal comes from a particle, the particle mass spectrum, and the bulk mass distribution derived from particle time-of-flight mode. Our results also show that while there is no size dependence to CE for SOA, particles that have passed through a thermodenuder have lower CE, implicating oxidation state and/or volatility as a controller of particle bounce.

The objective of this thesis was to further develop a methodology for surface tension measurement called Axisymmetric Drop Shape Analysisn(ADSA) and to adapt it to studies of lung surfactants, i.e. the material that coats and facilitates the functioning of the lungs of all mammals. The key property of a functioning lung surfactant is its surface tension, which can reach extremely low values. Such values are difficult to measure; but a certain configuration of ADSA, using a constrained sessile drop (ADSA--CSD), is capable of performing such measurements. Clinically, lung surfactant films can be altered from both sides, i.e. from the airspace as well as from the bulk liquid phase that carries the film. Therefore, being able to access the interface from both sides is important. Here, ADSA--CSD was redesigned to be used as a micro film balance allowing access to the interface from both gas- and liquid-side. This allows deposition from the gas side as well as complete exchange of the bulk liquid phase. The new design was used to study lung surfactant inhibition and inhibition reversal. A dynamic compression-relaxation model (CRM) was developed to describe the mechanical properties of lung surfactant films by investigating the response of surface tension to changes in surface area. The model evaluates the quality of lung surfactant preparations -- beyond the minimum surface tension value -- and calculates the film properties, i.e. elasticity, adsorption and relaxation, independent of the compression protocol. The accuracy of the surface tension measurement can depend on drop size. A detailed analysis of drop shapes and accuracy of measured surface tension values was performed using a shape parameter concept. Based on this analysis, the design of ADSA--CSD was optimized to facilitate more accurate measurements. The validity analysis was further extended to the more conventional pendant drop setup (ADSA--PD). An overall upgrade of both hardware and software of ADSA--CSD, together with extensive numerical work, is described and applied to facilitate a more efficient operation. Finally, it is noted that the ADSA--CSD setup developed here can be used for a wide range of colloid and surface chemical applications.

The objective of this thesis was to further develop a methodology for surface tension measurement called Axisymmetric Drop Shape Analysisn(ADSA) and to adapt it to studies of lung surfactants, i.e. the material that coats and facilitates the functioning of the lungs of all mammals. The key property of a functioning lung surfactant is its surface tension, which can reach extremely low values. Such values are difficult to measure; but a certain configuration of ADSA, using a constrained sessile drop (ADSA--CSD), is capable of performing such measurements. Clinically, lung surfactant films can be altered from both sides, i.e. from the airspace as well as from the bulk liquid phase that carries the film. Therefore, being able to access the interface from both sides is important. Here, ADSA--CSD was redesigned to be used as a micro film balance allowing access to the interface from both gas- and liquid-side. This allows deposition from the gas side as well as complete exchange of the bulk liquid phase. The new design was used to study lung surfactant inhibition and inhibition reversal. A dynamic compression-relaxation model (CRM) was developed to describe the mechanical properties of lung surfactant films by investigating the response of surface tension to changes in surface area. The model evaluates the quality of lung surfactant preparations -- beyond the minimum surface tension value -- and calculates the film properties, i.e. elasticity, adsorption and relaxation, independent of the compression protocol. The accuracy of the surface tension measurement can depend on drop size. A detailed analysis of drop shapes and accuracy of measured surface tension values was performed using a shape parameter concept. Based on this analysis, the design of ADSA--CSD was optimized to facilitate more accurate measurements. The validity analysis was further extended to the more conventional pendant drop setup (ADSA--PD). An overall upgrade of both hardware and software of ADSA--CSD, together with extensive numerical work, is described and applied to facilitate a more efficient operation. Finally, it is noted that the ADSA--CSD setup developed here can be used for a wide range of colloid and surface chemical applications.

The major aim of this thesis has been to contribute to the understanding of the CH$ sb2$/OH/NH$ sb2$ group interactions by means of studies of alcohol-amine mixtures in the gas and liquid phases. / To study these interactions in the gas phase a Burnett type equipment was designed, built and operated at low pressure, obtaining experimental pressure-temperature (P-T) data for various systems including alcohol-amylamine mixtures. The P-T data were reduced by a method developed in this work to give values of second virial coefficients. Measurements on known systems were in excellent agreement with values reported in the literature. A group contribution method for predicting pure compounds and interaction second virial coefficients is presented. This method is equal, or superior to methods already available. / To study the CH$ sb2$/OH/NH$ sb2$ group interactions in the liquid phase, vapor-liquid-equilibrium (VLE) experiments with alcohol-amylamine mixtures were carried out in a Van Ness type apparatus. The raw data were reduced by a novel model free method using the second virial coefficients obtained previously for these mixtures. A group contribution method for predicting vapor-liquid-equilibria of multicomponent multigroup mixtures is proposed. Excellent predictions are obtained with this method. / Finally, computer experiments of Lennard-Jones fluid mixtures were carried out to help in the understanding of the local composition concept. This concept is of fundamental importance not only in the models used in this work but also in numerous other solution models.

Thesis (Ph.D.)--York University, 2006. Graduate Programme in Earth and Space Science. / Typescript. Includes bibliographical references (leaves 181-195). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:NR19764

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (p. 169-185).