The ability to fabricate semiconductor wafers with spatially selected regions of different bandgap material is required for the fabrication of monolithic photonic integrated circuits (PIC's). Although this subject has been studied for three decades and many semiconductor engineering approaches have been proposed, the problem of achieving reproducible results has constantly challenged scientists and engineers. This concerns not only the techniques relaying on multiple sequential epitaxial growth and selective area epitaxy, but also the conventional quantum well intermixing (QWI) technique that has been investigated as a post-growth approach for bandgap engineering. Among different QWI techniques, those based on the use of different lasers appear to be attractive in the context of high-precision and the potential for cost-effective bandgap engineering. For instance, a tightly focused beam of the infrared (IR) laser could be used for the annealing of small regions of a semiconductor wafer comprising different quantum well (QW) or quantum dot (QD) microstructures. The precision of such an approach in delivering wafers with well defined regions of different bandgap material will depend on the ability to control the laser-induced temperature, dynamics of the heating-cooling process and the ability to take advantage of the bandgap engineering diagnostics. In the frame of this thesis, I have investigated IR laser-induced QWI processes in QW wafers comprising GaAs/A1GaAs and InP/InGaAsP microstructures and in InAs QD microstructures grown on InP substrates. For that purpose, I have designed and set up a 2-laser system for selective area rapid thermal annealing (Laser-RTA) of semiconductor wafers. The advantage of such an approach is that it allows carrying out annealing with heating-cooling rates unattainable with conventional RTA techniques, while a tightly focused beam of one of the IR lasers is used for `spot annealing'. These features have enabled me to introduce a new method for iterative bandgap engineering at selected areas (IBESA) of semiconductor wafers. The method proves the ability to deliver both GaAs and InP based QW/QD wafers with regions of different bandgap energy controlled to better than « 1nm of the spectral emission wavelength. The IBESA technique could be used for tuning the optical characteristics of particular regions of a QW wafer prepared for the fabrication of a PIC. Also, this approach has the potential for tuning the emission wavelength of individual QDs in wafers designed, e.g., for the fabrication of single photon emitters. In the 1st Chapter of the thesis, I provide a short review of the literature on QWI techniques and I introduce the Laser - RTA method. The 2nd Chapter is devoted to the description of the fundamental processes related to the absorption of laser light in semiconductors. I also discuss the results of the finite element method applied for modeling and semi-quantitative description of the Laser - RTA process. Details of the experimental setup and developed procedures are provided in the 3rd Chapter. The results concerning direct bandgap engineering and iterative bandgap engineering are discussed in the 4th and 5th Chapters, respectively.

HIV-NC is a multifunctional protein which plays an important role in almost every step of the retroviral life cycle. NC is essential in catalyzing stand transfers of HIV-1 reverse transcription, including the annealing of the transactivation response element (TAR) of the viral genome to the complementary TAR DNA in minus-strong-stop DNA. In this dissertation, the research starts with focus on elucidating the reaction mechanism of NC-facilitated TAR DNA/RNA annealing using single molecule spectroscopy (SMS) approaches. The results indicate that nucleation of TAR DNA/RNA annealing occurs in an encounter complex form in which one or two DNA/RNA strands in the partially open “Y” form associated with multiple NC molecules. This encounter complex leads to annealing through the 3’/5’ termini, namely “zipper” pathway and the annealing through the hairpin loop region, namely “kissing” pathway. By employing target oligonucleotides for specific TAR regions, we directly probed kinetic reversibility and the chaperone role of NC. Concentration-dependence of NC chaperoned melting and annealing of TAR hairpins was investigated and the results further support the proposed reaction mechanism. Additionally, we used a single-stranded DNA (ssDNA) as model to study ssDNA conformational change upon NC binding. Here we present observation of NC binding to d(TG)n and d(T)n, including NC effect on flexibility and conformation of these oligonucleotides chains. Our results reveal that the rigidity of ssDNA chain is dramatically reduced through interaction with NC. Meanwhile the results of NC dissociation experiments indicate the interaction of NC/ssDNA is complex and heterogeneous. Finally, we used SMS in vitro to systematically compare and contrast the RNA/protein interactions for the zinc-finger-binding-motif protein (NC) and the arginine-rich-binding-motif (ARM) protein (Tat) encoded by HIV-1. Tat and NC use different RNA binding motifs to recognize and interact with RNA hairpin, giving rise to very different changes in the RNA secondary structure upon protein binding. Competition experiments show that the presence of Tat can effectively inhibit the NC binding-induced local melting of TAR RNA hairpins. These results indicate that Tat specifically binds and stabilizes the TAR RNA hairpin structure, which likely inhibits the local melting of the hairpin induced by NC. / text

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This thesis is concerned with the study of morphology and properties of sub-micron thin Nafion® films. The motivation of the work arises from the need to characterize the 4 -10 nm thin ionomer films in the catalyst layer of polymer electrolyte fuel cell (PEFC). A protocol for the fabrication of self-assembled ultra-thin Nafion® films on planar substrates was successfully developed. Films of thickness ranging 4 nm-300 nm, determined by three different techniques - variable angle spectroscopy ellipsometry (VASE), atomic force microscope (AFM) and x-ray photo-electron spectroscopy (XPS), could be reproducibly generated on SiO2/Si wafer. The 4 nm thin film is one of the thinnest, continuous film of Nafion® ever reported. This is the first time that the structure/properties of such thin Nafion® film have been investigated. An interesting finding is the thickness-dependent structure and property of these films. Films with thickness <55 nm exhibited hydrophilic-free surface but thicker films (>55 nm) had hydrophobic surface. Similarly, sub-55 nm films had a lower and thickness-independent protonic conductivity compared to thicker films that exhibited thickness-dependent conductivity. Anomalously high water uptake (by quartz crystal microbalance) and swelling (by ellipsometry) of sub-55nm films indicate that low conductivity is not due to low water content However, differences in surface morphology were observed by the AFM phase contrast analysis. The lack of ionic domain was also observed in the thinner films (4-30 nm) from the grazing incidence small x-ray scattering (GISAXS) experiments. Thermal annealing over a range of temperature (110-160 oC) revealed a dramatic switching of the film surface from hydrophilic to hydrophobic was observed for sub-55 nm films with lower thickness film requiring higher annealing temperature. Bulk proton conductivity was significantly reduced after annealing for all films. An interesting finding was the regeneration of conductivity after to prolonged liquid water exposure and a corresponding switching back of the surface to hydrophilic. The thickness-dependent structure/property of ultra-thin Nafion® films is attributed to substrate induced confinement effect. Self-assembly of Nafion® on various substrates (SiO2, carbon, Pt and Au) was studied. The ionomer/substrate interaction and resulting film morphology followed a trend with respect to substrate surface energies and Nafion® dispersion compositions. / Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2013-09-29 12:36:19.05

The field of modelling and processing of 'images' has fairly recently become important, even crucial, to areas of science, medicine, and engineering. The inevitable explosion of imaging modalities and approaches stemming from this fact has become a rich source of mathematical applications. <br /><br /> 'Imaging' is quite broad, and suffers somewhat from this broadness. The general question of 'what is an image?' or perhaps 'what is a natural image?' turns out to be difficult to address. To make real headway one may need to strongly constrain the class of images being considered, as will be done in part of this thesis. On the other hand there are general principles that can guide research in many areas. One such principle considered is the assertion that (classes of) images have multiscale relationships, whether at a pixel level, between features, or other variants. There are both practical (in terms of computational complexity) and more philosophical reasons (mimicking the human visual system, for example) that suggest looking at such methods. Looking at scaling relationships may also have the advantage of opening a problem up to many mathematical tools. <br /><br /> This thesis will detail two investigations into multiscale relationships, in quite different areas. One will involve Iterated Function Systems (IFS), and the other a stochastic approach to reconstruction of binary images (binary phase descriptions of porous media). The use of IFS in this context, which has often been called 'fractal image coding', has been primarily viewed as an image compression technique. We will re-visit this approach, proposing it as a more general tool. Some study of the implications of that idea will be presented, along with applications inferred by the results. In the area of reconstruction of binary porous media, a novel, multiscale, hierarchical annealing approach is proposed and investigated.

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In this thesis, the structural, optical, and electrical properties of wurtzite MgxZn1-xO:Al and MgxZn1-xO:Ga thin films have been investigated in dependence on Mg and dopant concentration. Among the transparent conductive oxides (TCOs), ZnO based compounds have gained renewed interest as a transparent electrode for large scale applications such as defroster windows, at panel displays, touch screens, and thin film solar cells due to low material and processing cost, non-toxicity, and suitable physical properties. In general, these applications require transparent electrodes with lowest possible resistivity of rho < 10^-3 Ohmcm and lower [1]. Recently, it has been reported that Ga and Al doped ZnO thin films can be deposited with respective resistivity of 5x10^-5 Ohmcm [2] and 3 x10^-5 Ohmcm [3] which are similar to the data obtained for other practical TCOs, i.e. the resistivity of about 4x 10^-5 Ohmcm for Sn doped In2O3 (ITO) thin films [4]. Moreover, the bandgap of ZnO can be increased by alloying with Mg offering band alignment between transparent electrode and active (or buffer) layer of the device, e.g. Cu(In,Ga)Se2 solar cells [5]. The tunable bandgap of these transparent electrodes can further increase the efficiency of the devices by avoiding energy losses in the interface region of the layers. From this point of view, this work has been aimed to investigate the doping efficiency and limits in transparent conductive (Mg,Zn)O alloys. For this purpose, the samples investigated in this work have been grown by pulsed-laser deposition (PLD) using a novel, continuous composition spread method (CCS). In general, this method allows to grow thin films with lateral composition gradient(s) [6, 7]. All MgxZn1-xO:Al and MgxZn1-xO:Ga thin films have been deposited on 2-inch in diameter glass, c- or r-plane sapphire substrates using threefold segmented PLD targets in order to grow thin films with two perpendicular, lateral composition gradients, i.e. the Mg composition is varied in one direction whereas the Al/Ga concentration is varied in a perpendicular direction [7, 8]. In order to investigate the influence of the temperature, samples grown at different substrate temperatures in the range of 25 to 600 C were investigated. The optical and electrical measurements have been carried out on (5x 5)mm^2 samples that were cut from the CCS wafers along the respective composition gradients, i.e. Mg and Al/Ga contents. Subsequently, physical properties of thin films have been analyzed for a large range of Al/Ga content between 0.5 and 7 at.%, which corresponds to doping concentrations between 2x 10^20 and 3x 10^21 cm^-3, for different Mg contents x(Mg) ranging from 0.01 to 0.1. It has been found that practically the limiting the dopant concentrations is about 2 x10^21 cm^-3. Further, the electrical data suggests, that the compensating intrinsic defect is doubly chargeable hinting to the zinc vacancy (V_Zn) as microscopic origin. Increasing the dopant concentration above 2 x10^21 cm^-3 leads to a degradation of electrical and structural properties [8]. Further, the influence of growth and annealing temperatures on structural, electrical and optical properties of the films has been studied. For that purpose, Al and Ga doped (2.5 at.% = 1x10^21 cm^-3) Mg0.05Zn0.95O thin films have been chosen from CCS samples grown at T_g = (25 - 600) C . For both doping series, the samples grown at higher temperatures exhibit better crystalline quality compared to the samples grown at lower growth temperatures. As a result, samples grown at higher temperatures reveal higher Hall mobility. For the Al-doping series, the highest free charge carrier density of n = 8.2x 10^20 cm^-3 was obtained for an Mg0.05Zn0.95O:Al thin film grown at 200 C, with corresponding Hall mobility of mu = 13.3 cm^2/Vs, a resistivity of rho = 5.7x10^-4 Ohmcm, and optical bandgap of E_g = 3.8 eV. Interestingly, the free charge carrier density of n = (5 - 8) x 10^20 cm^-3 for samples grown with T_g > 300 C is clearly higher than the value of n = 1.25 x 10^20 cm^-3 that was obtained for the high temperature grown sample, i.e. at T_g = 600 C. Furthermore, for all T_g, Al-doped films have a higher doping efficiency than the Ga-doped counterparts. In order to look deeper into the microscopic origin of this behavior, the samples were post-annealed in vacuum at 400 C. Experimental results showed that the free charge carrier density of Al-doped samples first decreased and saturated afterward with increasing annealing time. On the other hand, the free charge carrier density of the Ga-doped samples first slightly increased and saturated with increasing annealing time. For both doping series, the saturation value of n ~ 1 x 10^20 cm^-3 was very close to the data that has been observed for (i) high temperature grown samples and (ii) the solubility limit of Al in ZnO of 0.3 at.% = 1.2x 10^20 cm^-3, that has been determined by Shirouzu et al. for high temperature grown (T_g > 600 C) Al-doped ZnO [9]. Correspondingly, the optical bandgap also changed, i.e. increased (decreased) for Al- (Ga-) doping series, and approached a constant value of 3.5 0 +- 0.1 eV which is explained by generation of acceptor-like compensating defects, and the solubility limit of the dopants. From XRD data, no secondary phases were found for as-grown and post-annealed films. However, the slight improvement of crystalline quality has been observed on post-annealed samples. Further, it has been shown that the growth and annealing temperatures are important as they strongly affect the metastable state of the solid solution that samples grown at low temperature represent. The low solubility limit of the dopants, i.e. 0.3 at.% for Al in ZnO under equilibrium condition, can be increased by preparing samples by non-equilibrium growth techniques [10]. This is also consistent with experimental results of this work that Al- as well as Ga-doped metastable ZnO and (Mg,Zn)O thin films can be prepared with highest possible doping efficiency for the dopant concentration up to 2.5 at.% when growth or annealing temperatures below 400 C are used.

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete measurements. In the second part, we focus on thereconstruction of signal transduction mechanisms in the signaling pathway components. Wepropose gene set based approaches for inferring the structure of a signaling pathway.First, we present a constrained multivariate Gaussian model, referred to as the informed-case model, for estimating the correlation structure from replicated and complete molecular profiling data. Informed-case model generalizes previously known blind-case modelby accommodating prior knowledge of replication mechanisms. Second, we generalize theblind-case model by designing a two-component mixture model. Our idea is to strike anoptimal balance between a fully constrained correlation structure and an unconstrained one.Third, we develop an Expectation-Maximization algorithm to infer the underlying correlation structure from replicated molecular profiling data with missing (incomplete) measurements.We utilize our correlation estimators for clustering real-world replicated complete and incompletemolecular profiling data sets. The above three components constitute the first partof the dissertation. For the structural inference of signaling pathways, we hypothesize a directed signal pathway structure as an ensemble of overlapping and linear signal transduction events. We then propose two algorithms to reverse engineer the underlying signaling pathway structure using unordered gene sets corresponding to signal transduction events. Throughout we treat gene sets as variables and the associated gene orderings as random.The first algorithm has been developed under the Gibbs sampling framework and the secondalgorithm utilizes the framework of simulated annealing. Finally, we summarize our findingsand discuss possible future directions.

Seismic inversion using a global optimization algorithm is a non-linear, model-driven process. It yields an optimal solution of the cost function – reflectivity/acoustic impedance, when prior information is sparse. The inversion result offers detailed interpretations of thin layers, internal stratigraphy, and lateral continuity and connectivity of sand bodies. This study compared two stable and robust global optimization techniques, Simulated Annealing (SA) and Basis Pursuit Inversion (BPI) as applied to post-stack seismic data from the Gulf of Mexico. Both methods use different routines and constraints to search for the minimum error energy function. Estimation of inversion parameters in SA is rigorous and more reliable because it depends on prior knowledge of subsurface geology. The BPI algorithm is a more robust deterministic process. It was developed as an alternative method to incorporating a priori information. Results for the Gulf of Mexico show that BPI gives a better stratigraphic and structural actualization due to its capacity to delineate layers thinner than the tuning thickness. The SA algorithm generates both absolute and relative impedances, which provide both qualitative and quantitative characterization of thin-bed reservoirs.