Trace gases and aerosols, or suspended liquid and solid material in the atmosphere, have significant climatological and societal impacts; consequently, accurate representation of their contribution to atmospheric composition is vital to predicting climate change and informing policy actions. Sensitivity analysis allows scientists and environmental decision makers alike to ascertain the role a specific component of the very complex system that is the atmosphere of the Earth. Anthropogenic and natural emissions of gases and aerosol are transported by winds and interact with sunlight, allowing significant transformation before these species reach the end of their atmospheric life on land or in water. The adjoint-based sensitivity method assesses the relative importance of each emissions source to selected results of interest, including aerosol and cloud droplet concentration. In this work, the adjoint of a comprehensive inorganic aerosol thermodynamic equilibrium model was produced to improve the representativeness of regional and global chemical transport modeling. Furthermore, a global chemical transport model adjoint equipped with the adjoint of a cloud droplet activation parameterization was used to explore the footprint of emissions contributing to current and potential future cloud droplet concentrations, which impact the radiative balance of the earth. In future work, these sensitivity relationships can be exploited in optimization frameworks for assimilation of observations of the system, such as satellite-based or in situ measurements of aerosol or precursor trace gas concentrations.

Natural and synthetic heterocyclic cations that bind to the DNA minor groove have demonstrated effectiveness as therapeutic agents for cancer, parasitic and viral diseases, as well as powerful probes for use to extend our fundamental understanding of DNA molecular recognition. Crystal and NMR structures with a variety of minor groove binding compounds have shed light on the structural varieties of these systems, the important solvent molecules in the complexes, and the induced fit effects for binding of both DNA and the bound small molecule. Topics of specific importance in DNA recognition are the development of a greater variety of cell-permeable minor groove agents that have increased DNA binding sequence selectivity. In this dissertation, the structural and energetic basis of the interaction between DNA and minor groove binders has been systematically investigated. A set of powerful and complementary biophysical methods have been used: gel electrophoresis with ligation ladder assay, circular dichroism, mass spectrometry, surface plasmon resonance and isothermal titration calorimetry have been applied to determine the binding stoichiometry, binding affinity, kinetics and thermodynamics, and also the structural influence that minor groove binders can have on DNA. The results of several minor groove complexes clearly show that based on DNA sequences, minor groove binders can have multiple binding modes and consequently affect the geometry of DNA minor groove and the overall DNA curvature in distinct manners. In addition, the binding enthalpy of a minor groove binder is essentially salt concentration and binding mode independent. Besides the investigation of DNA-minor groove binder complex, the binding and inhibition of transcription factor PU.1 has also been studied. The highly positive charged PU.1 targets DNA by inserting an α-helix in the major groove of the 5’-GGAA-3’ site, and displays a strong salt concentration dependency. A set of minor groove binders have been rationally designed based on the high-affinity DNA sequence for PU.1 to target the flanking sequences of the 5’-GGAA-3’ site. They display a structure-related PU.1 inhibition efficacy. This work demonstrates that minor groove binders are capable of modulating PU.1 by targeting the opposite groove and supports future efforts to develop agents for other transcription factors.

It is well established that non-equilibrium flows cannot properly be described by traditional hydrodynamics, namely, the Navier-Stokes-Fourier (NSF) equations. Such flows occur, for example, in micro-electro-mechanical systems (MEMS), and ultra vacuum systems, where the dimensions of the devices are comparable to the mean free path of a gas molecule. Therefore, the study of non-equilibrium effects in gas flows is extremely important. The general interest of the present study is to explore boundary value problems for moderately rarefied gas flows, with an emphasis on numerical solutions of the regularized 13--moment equations (R13). Boundary conditions for the moment equations are derived based on either phenomenological principles or on microscopic gas-surface scattering models, e.g., Maxwell's accommodation model and the isotropic scattering model. Using asymptotic analysis, several non-linear terms in the R13 equations are transformed into algebraic terms. The reduced equations allow us to obtain numerical solutions for multidimensional boundary value problems, with the same set of boundary conditions for the linearized and fully non-linear equations. Some basic flow configurations are employed to investigate steady and unsteady rarefaction effects in rarefied gas flows, namely, planar and cylindrical Couette flow, stationary heat transfer between two plates, unsteady and oscillatory Couette flow. A comparison with the corresponding results obtained previously by the DSMC method is performed. The influence of rarefaction effects in the lid driven cavity problem is investigated. Solutions obtained from several macroscopic models, in particular the classical NSF equations with jump and slip boundary conditions, and the R13--moment equations are compared. The R13 results compare well with those obtained from more costly solvers for rarefied gas dynamics, such as the Direct Simulation Monte Carlo (DSMC) method. Flow and heat transfer in a bottom heated square cavity in a moderately rarefied gas are investigated using the R13 and NSF equations. The results obtained are compared with those from the DSMC method with emphasis on understanding thermal flow characteristics from the slip flow to the early transition regime. The R13 theory gives satisfying results including flow patterns in fair agreement with DSMC in the transition regime, which the conventional Navier-Stokes-Fourier equations are not able to capture. / Graduate / 0548 / anirudh@uvic.ca

This thesis is concerned with a project to apply the method of pressure modulation radiometry to measurements of the temperature and water vapour distributions in the atmosphere of Mars. The technique has already been used successfully to measure temperature (and occasionally composition) in the atmospheres of Earth and Venus. Two pressure modulators, containing carbon dioxide and water vapour respectively, are used in the Pressure Modulator Infrared Radiometer (PMIRR), on the payload of Mars Observer, scheduled for launch in September 1992. The composition of the Martian atmosphere is almost pure CO2, so the emission lines are unusually broad, so that the mean pressure in the CO2 modulator has to be much larger than for previous modulators, thus increasing the power consumption. The limited power available in a Martian spacecraft requires that the power consumption of the pressure modulator and drive be minimized. As a result a high­efficiency drive circuit was designed and developed. Water vapour is of major importance to the Martian environment and there are several outstanding questions about its behaviour. Measurements using the pressure modulator technique for terrestrial water vapour measurements have had limited success, raising questions about its suitability for condensible, affinitive molecules. A new model of the thermodynamics of pressure modulators was developed to predict their mechanical and spectroscopic behaviour, and spectroscopic measurements of the pressure modulator cell transmission, with high spectral and temporal resolution, using a tunable diode laser spectrometer (TDLS), were performed. The measured transmission agrees well with the predictions of the model, indicating that pressure modulation radiometry can be applied to measurements of water vapour, giving confidence in the successful study of Martian climatology by the PMIRR instrument.

A dynamic model was developed for the distillation mechanism of the Darlington Tritium Removal Facility. The model was created using the commercial software package MATLAB/Simulink. The goal was to use such a model to predict the system behaviour for use in control analysis. The distillation system was first divided into individual components including columns, condensers, controllers, heaters and the hydraulic network. Flow streams were then developed to transfer enthalpy, pressure and mass flow rate between the components. The model was able to perform various plant transients for validation and analysis purposes. A comparison of the different controllers was made with the introduction of various disturbances to the system. Also, the effect of the system disturbances when isolated from the transients was studied using the same controllers. Studying different plant transients and disturbances under each controller enabled a comparative analysis.

A dynamic model was developed for the distillation mechanism of the Darlington Tritium Removal Facility. The model was created using the commercial software package MATLAB/Simulink. The goal was to use such a model to predict the system behaviour for use in control analysis. The distillation system was first divided into individual components including columns, condensers, controllers, heaters and the hydraulic network. Flow streams were then developed to transfer enthalpy, pressure and mass flow rate between the components. The model was able to perform various plant transients for validation and analysis purposes. A comparison of the different controllers was made with the introduction of various disturbances to the system. Also, the effect of the system disturbances when isolated from the transients was studied using the same controllers. Studying different plant transients and disturbances under each controller enabled a comparative analysis.

RNA aptamers are in vitro sequences of RNA that have a high affinity for their target ligand. They have applications in therapeutics, biosensors and molecular machines. While the practical applications of aptamers are increasing, it is important to study their structure and thermodynamics to improve the understanding of these molecular tools. The malachite green aptamer (MGA) provides a model system to study the interactions between aptamer and ligand that do not involve hydrogen bonding between ligand and receptor. While the original application of this aptamer was abandoned, study of the MGA binding pocket revealed an electronegative environment that was harnessed for catalysis. MGA binding also supported the notion that aptamers bind by adaptive binding. Adaptive binding is the ability of molecules to mold themselves around the structure of a ligand thereby incorporating it into their three-dimensional fold. To further expand our understanding of MGA binding and to clarify conflicting reports of affinities, we conducted isothermal calorimetry binding studies. The results reveal that the entropy of complex formation plays a large role in determining binding affinity and ligand specificity. This data combined with previous structural studies show that metal ions are required to stabilize the complexes with non-native ligands, whereas, the complex with the original selection target is stable at low salt and in the absence of divalent metal ions. Next, competitive binding studies using isothermal titration calorimetry were conducted with the aim of understanding the adaptive nature of RNA. The results of these studies reveal that there are limits to the adaptability of the aptamer. Binding of one type of ligand reduces the affinity of the aptamer pocket to a differently shaped ligand, even if this second ligand has a significantly higher affinity. The ability of MGA to change ligand preference based on buffer conditions, and the previously reported catalysis suggested that RNA may have a potential supporting multiple functions in the same molecule. To investigate this possibility we attempted to select an aptamer that supports both ligand binding and catalysis. By conducting both a DNA and RNA selection we hoped to add to the iv collection of DNA and RNA aptamers selected for the same target. There are currently too few of these to determine if any correlation can be made between DNA and RNA sequences that bind the same target. The target of the selection was fluorescein diacetate (FDA), which was chosen with the aim that it would allow the exploration of the inherent potential of the selected aptamer to cleave FDA to fluorescein. The RNA selection proved to be more successful and an attempt was made to characterize the binding of the aptamer to its target fluorescein diacetate. Unfortunately there were complications with the binding assays, but future work is proposed that should address the issues. In order to expand the MGA catalytic repertoire attempts were made to synthesize new ligands that could exploit the catalytic potential of the MGA binding pocket. Unfortunately these attempts were unsuccessful, however further attempts are recommended. The MGA used in this study was transcribed in vitro using T7 RNA polymerase. This process is known to add extra nucleotides to the end of the transcription product. Attempts were made to eliminate the n+1 product by introducing a ribozyme or DNAzyme. These were met with difficulties resulting in low yield, however mass spectrometry revealed that n and n+1 MGA bind to ligand. This, along with secondary structure prediction suggests that MGA n+1 behaves the same as n. Overall, the results presented here provide insights into the capabilities of RNA aptamers with respect to ligand binding and catalysis.

Solar assisted single-stage absorption heat pump (AHP) was used to supply energy to a floor-heating system by using the exergy methods. An existing duplex-house,in Ankara, with a heating load of 25.5 kW was analysed. Heating loads of the spaces in the building were calculated and a floor heating panel was modelled for each space leading to the capacity of the AHP before it was designed. Solar energy was delivered to the evaporator and high temperature heat input delivered to the genarator are met by auxiliary units operating with natural gas.The solar energy gained by flat-plate collectors was circulated through AHP.The anaysis performed according to the storage tank temperature reference value if the water temperature leaving the storage tank exceeds a predetermined value it is directly circulated through the floor heating system. Exergue analysis were carried out with Mathcad program. Exergy analysis showed that irreversibility have an impact on absorption system performance.This study indicated which components in the system need to be improved thermally.A design procedure has been applied to a water-lithium-bromide absorption heat pump cycle and an optimisation procedure that consists of determinig the enthalpy, entropy ,exergy, temperature, mass flow rate in each component and coeficient of performance and exergetic coefficient of performance has been performed and tabulated.

The objective of this study is to analyze theoretically the laminar film condensation of water vapor flowing on a sphere. For this purpose, the problem was handled by including all of the two-phase boundary layer parameters such as gravity, effect of vapor shear, inertia, energy convection and pressure gradient. For this full two-phase boundary layer system, the boundary layer equations, boundary conditions and the interfacial conditions were first analyzed, and then discretized. A computer program in Mathcad, solving these discretized equations, was written to obtain the velocity and temperature profiles within the condensate, the velocity profiles within the vapor, the condensate film thickness and the local Nusselt number. The effects of pressure gradient, gravity, vapor oncoming velocity and sphere radius on these parameters were examined. By alternating the formulation of the problem, the results for the flow over a horizontal cylinder were obtained. These results were then compared with those for the sphere. Finally, the results for the system with Mercury vapor flowing on a sphere were obtained. All of these results were represented as diagrams and tables, and were discussed at the end of the study.

This thesis analyzes the nonextensive generalization of Boltzmann-Gibbs statistics and study its applications to some physical models such as isotropic rigid and non-rigid rotators. The thesis will also try to show what kind of internal energy constraint must be chosen for entropy optimization in a mathematically consistent manner.