About 50% of cancer patients are treated with X-ray radiation therapy; however, with current treatment feedback, the effects and the efficacy of the treatment are generally detected several weeks/months after treatment completion. This makes the adjustment of the treatment based on early response, and identification of non-responding patients, nearly impossible. In this thesis a novel method combining optical coherence tomography and a gamut of image analysis methods is explored as a potential approach to detecting tissue variability. Applying texture analysis to the optical coherence tomography images may allow for the tracking of radiation therapy induced cell microstructural changes in cancer patients and help in the adjustment of treatment based on early response.

About 50% of cancer patients are treated with X-ray radiation therapy; however, with current treatment feedback, the effects and the efficacy of the treatment are generally detected several weeks/months after treatment completion. This makes the adjustment of the treatment based on early response, and identification of non-responding patients, nearly impossible. In this thesis a novel method combining optical coherence tomography and a gamut of image analysis methods is explored as a potential approach to detecting tissue variability. Applying texture analysis to the optical coherence tomography images may allow for the tracking of radiation therapy induced cell microstructural changes in cancer patients and help in the adjustment of treatment based on early response.

Introduction Temperature modeling using Finite Element Analysis (FEA) is widely used by particle beam-line designers as a useful tool to determine the thermal performance of an irradiated target system. A comparison study was performed between FEA calculated temperatures on platinum with experimental results using direct thermocouple measurements. The aims are to determine the best beam model for future solid target design, determine the maximum target current for different target materials and the temperature tolerance for any modification to our existing solid targetry system. Material and Methods The theoretical temperature of the target sys-tem was determined using SolidWorks 2013 with Flow Simulation Analysis (FSA) module. The FSA module determines the maximum temperature inside the target material given the global conditions (material specification, flow rates, boundary conditions, etc.) for a given target current. The proton beam was modeled as a volumetric heat source inside the target material based on the distribution of energy loss in the material along the beam axis. The method used by Comor, et al1 was used in this study. The method segmented the target material into five individual layers, each layer being 50 m thick. The energy lost per layer was calculated using SRIM3 and converted into the power lost per layer. A thickness of 250 μm of platinum completely stops the impinging proton beam at 11.5 MeV with the highest deposition of power per layer corresponding to the Bragg peak. The target material used in the simulation reflects the physical target disk used for temperature measurements (platinum, dia. 25.0 mm, thickness 2.0 mm) with two K-type thermocouples (dia. 0.5 mm, stainless steel sheath) embedded in the platinum disk. One thermocouple is located in the geometric center, while the other is located at a radial position 8 mm from center. The outer thermocouple is to determine the peripheral temperature near the o-ring seal. Temperature was maintained below the melting point for the material (Viton®, melting point 220 °C) during the irradiation to ensure the integrity of the water cooling system. The solid targetry system used in this study is an in-house built, significantly modified version2 of a published design1. The solid target system is mounted onto an 18/18MeV IBA Cyclotron with dual ion source, on a 300mm beam-line with no internal optics or steering magnets. A graphite collimator reduces the beam to 10mm in diameter and a degrader is used to reduce the proton beam energy to 11.5 MeV, considered suitable for production of radiometal PET isotopes 89Zr and 64Cu. Temperature was measured with and without the 300 mm beam-line to compare the effects of beam divergence on the solid target (FIGS. 1 and 2). The experiment was conducted using both H− ion sources with different ion-to-puller extraction gaps (ion source 1 is 1.55 mm with ion source 2 at 1.90 mm). The setting of the ion-to-puller gap changes the focusing of the accelerated beam inside the cavity. Results and Discussion The segmented beam model was used to calculate the temperature on and within the target, as well as the maximum temperature of the bulk material. The first segment is the leading segment of the material irradiated by the incident proton beam. Results are shown in TABLE 2. Target temperatures were measured experimentally under two different conditions; target attached at the end of a 300mm beam-line and target attached directly to the cyclotron. The temperature was measured experimentally using the platinum disk with 2 thermocouples inside the bulk target material irradiated on the end of a 300mm beam-line. The measured temperature is shown in TABLE 2. The variation between ion source 1 and 2 for the temperature measured in the center was 11–15 %, while the variation on the radial position was 2–6 %. A smaller ion-to-puller extraction distance (ion source 1) reduces the cross-sectional area of the accelerated beam; the consequent high proton current density (10mm diameter collimated beam) increases the temperature inside the bulk material for a fixed target current. The highest observed radial temperature was 93 °C, with target current of 50 μA using ion source 1. This is well below the melting point for the o-ring seal. The temperature measured experimentally using the same platinum disk with no beam-line is shown in TABLE 4. A temperature difference of up to 7 % was measured between ion source 1 and 2 at the exit port without the beam-line, while the maximum variation on the radial position was 3 %. A comparison between the calculated theoretical and measured temperatures is shown in FIGS. 3 to 6. The temperatures calculated by the FEA model underestimate the temperature regardless of target position (with or without the beam-line) and for both ion sources. The temperature difference between the FEA model and the experimental results increases with increasing target currents. As shown in Figure 3, at the target center the FEA model underestimated the temperature by 22–32 % for ion source 1 and 13–22 % for ion source 2. This is consistent with the difference between the two ion sources due to the difference in the ion-to-puller gap size. With the target mounted at the exit port the theoretical and measured temperature for the center of the platinum disk is shown in FIGURE 4. The FEA model underestimates the temperature at the center of the platinum disc by 2–10 % for both ion sources. As shown with the previous experiment, the margin of error increases with increasing target current. Comparison between FIGS. 3 and 4 shows the measured temperature at the center of the platinum disk is significantly lower when the target is attached to exit port of the cyclotron. Localised area of high current density (hot spots) is not registered as higher temperature in the bulk material. True temperature inside the bulk material is highly dependent on the thermal conductivity of the target material and the resolution of the thermocouple. The cross-sectional area of the beam ‘hot-spot’ will be greater due to beam divergence at the end of the beam line compared with the exit port. The ‘hot’ area of the expanded beam becomes a significant portion of the overall collimated beam (collimator dia. 10.0 mm). A more uniform beam profile (less heterogeneity) evenly distributed the area of high current density across the disk surface, effectively increasing the temperature of the bulk material while decreasing the sensitivity required to measure the true temperature. As observed from this comparative study it appears that a more homogeneous current density leads to a higher temperature measurement at the target center. With the solid target at the end of the beam-line, target current lost on the collimator and beam-line was >55%. The effect of beam divergence is clearly observed in TABLE 5. With the target mounted directly at the exit port the current lost was reduced to < 40 %. Although the average proton current density is the same for any set target current, irrespective of target position, the contribution of the peripheral beam to the total target current should not be underestimated. A loss of ~40 μA on the collimator and beam-line places greater reliance on the center of the ‘hot’ beam to maintain the same target current. The temperature at the radial position (FIG. 5) observes the same trend as for the temperature measured in the center. The error increases for higher target currents and the FEA model underestimated the temperature by 19–40 %. The error at this location is due partly to the model’s assumption of a uniform heat source, applied to the material on a single axis (perpendicular to the material surface) and does not account for any scattering or divergence of the incident proton beam. FIGURE 6 shows that the FEA model underestimated the radial temperature by 16–37 %, when the target is connected to the exit port, for reasons discussed previously. Comparison with FIG. 5 (target on the beam-line) shows the same margin of error between the FEA and the experimental results (19–40 %). The temperature difference between the FEA model and measured temperature at the radial position is independent of the beam profile and beam divergence. The FEA model underestimated the temperature at the radial location with or without the beam-line and for both ion sources. The significance difference in temperature between the FEA model and the experimental is due to our model assumption that the maximum radial temperature is on the irradiated surface and not inside the material corresponding to the layer with the maximum energy lost. In addition, the FEA model does not ac-count for the divergence of the proton beam as it travels through the material. Given the temperature at 50 μA target current is > 90 °C (TABLES 3 and 4) we have capped the experi-ment below this point to prevent any damage the o-ring seal. Conclusion The segmented FEA model was inadequate in determining the temperature for the target at the end of a 300mm beam-line (> 30 % difference). A combination of beam divergence and greater uniform coverage of high current density beam resulted in a higher than predicted temperature reading. However, the segmented FEA model provides a good estimation (< 10 % difference) for the observed temperature of the bulk material at the exit port. The simplistic FEA model was unable estimate the temperature at the radial position (~ 40 % difference) regardless of ion source or target position. A comparison between the two ion sources with different ion-to-puller extraction gap, leading to different focusing of the accelerated beam yield minimal temperature difference. Although a 15% difference was observed between the ion sources at the end of the beam-line, a major contributing factor is beam divergence beyond the magnetic field rather than the beam size of the accelerated beam. Further studies are underway to determine the beam profile (quantitatively using radiographic film), quantify the contribution of the peripheral beam to the total beam current by comparing different size collimators and to investigate other FEA models by applying different beam models (heterogeneous and homogeneous beam) and different heat sources (surface vs. volumetric). Currently the RAPID Lab solid targetry is placed at the end of the beam-line for easy loading and unloading, since multiple target irradiations are performed per month2. However, RAPID is presently developing a new solid targetry sys-tem which eliminates the need for a beam-line and will be able to manage a maximum extracted target current of 150 μA.

Photovoltaic devices are receiving growing interest in both industry and research institutions due to the great demand for clean and renewable energy. Among all types of solar cells, cadmium sulfide (CdS) – cadmium telluride (CdTe) and cadmium sulfide (CdS) - copper indium diselenide (CuInSe2 or CIS) heterojunctions based thin film solar cells are of great interest due to their high efficiency and low cost. Further improvement in power conversion efficiency over the traditional device structure can be achieved by tuning the optical and electric properties of the light absorption layer as well as the window layer, utilizing nano template-assisted patterning and fabrication. In this dissertation, simulation and calculation of photocurrent generation in nanowires (NW) based heterojunction structure indicated that an estimated 25% improvement in power conversion efficiency can be expected in nano CdS – CdTe solar cells. Two novel device configurations for CdTe solar cells were developed where the traditional thin film CdS window layer was replaced by nanowires of CdS, embedded in aluminum oxide matrix or free standing. Nanostructured devices of the two designs were fabricated and a power conversion efficiency value of 6.5% was achieved. Porous anodic aluminum oxide (AAO) was used as the template for device fabrication. A technology for removing the residual aluminum oxide barrier layer between indium tin oxide (ITO) substrate and AAO pores was developed. Causes and remedies for the non-uniform barrier layer were investigated, and barrier-free AAO on ITO substrate were obtained. Also, vertically aligned nanowire arrays of CIS of controllable diameter and length were produced by simultaneously electrodepositing Cu, In and Se from an acid bath into the AAO pores formed on top of an aluminum sheet. Ohmic contact to CIS was formed by depositing a 100 nm thick gold layer on top and thus a Schottky diode device of the Au/CIS nanowires/Al configuration was obtained. Material properties of all these nanowires were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), absorption measurement. Current-voltage (I-V), capacitance-voltage (C-V) and low-temperature measurements were performed for all types of devices and the results were analyzed to advance the understanding of electron transport in these nano-structured devices.

Theoretical and experimental results show that the performance of a load-bearing surface in hydrodynamic lubrication may be enhanced by engineering a definable surface texture onto the surface. These surface textures are in the form of protrusions (positive asperities) or cavities (negative asperities) of known size and geometry. The benefits of such surface textures include lower friction torque, higher load capacity and lower operating temperatures. This Thesis details a fabrication process to manufacture such surface textures/asperities on flat surfaces. The asperities are fabricated using a UV photolithography process followed by electroplating. A complete surface characterization is done to evaluate the effectiveness of the manufacturing process. From the characterization results, some errors in asperity geometry are identified and statistically quantified. These errors are found to be normally distributed and the random surface roughness is 1 to 3 orders of magnitude less than the deterministic feature size. The accuracy of the manufacturing process for fabricating the asperities was found to lie within 6.5 % of the desired value over all the errors studied. Finally, a sensitivity analysis is done to theoretically evaluate the effect of some of these errors in the hydrodynamic lubrication regime.

Recent advances in nano technology have opened doors to several next generation devices and sensors. Characterizing nano particles and structures in a simple and effective way is imperative for monitoring and detecting processes at nano scale in a variety of environments. In recent years, the problem of studying nano particle interactions with surface plasmons or evanescent waves has gained significant interest. Here, a numerical model is presented to characterize nano-size particles and agglomerates near a metal or a dielectric interface. The methodology is based on a hybrid method, where the T-matrix approach is coupled with the image theory. The far field scattering patterns of single particles and agglomerates subjected to surface plasmons/evanescent waves are obtained. The approach utilizes the vector spherical harmonics for the incident and scattered fields relating them through a T-matrix. Effects of size, shape and orientation of the cluster on their scattering patterns are studied. An effort is made to distinguish particle characteristics from the scattering information obtained at certain observation angles. Understanding these scattering patterns is critical for the design of sensors using the surface plasmon scattering technique to monitor nano self assembly processes

The deterministic microasperities play a vital role in reducing the coefficient of friction and wear of thrust surfaces and improve the tribological properties of the surfaces. Deterministic microasperities have a specific pattern in terms of size, shape and spacing. These specified geometries are controllable and repeatable. The microasperities are micron scaled asperities and cavities on a surface that form the surface roughness. The present thesis shows the detailed process to fabricate the deterministic microasperities on thrust surfaces, i.e. stainless substrate, using micro-fabrication processes such as lapping and ultra-violet photolithography in combination with an electroplating (nickel) process. A Novel alignment technique is used to align the photomask with the substrate to get repeatable and aligned patterns on the thrust surface. Deterministic microasperities are characterized by using precision instruments such as an Optical profilometer, Scanning Electron Microscope (SEM) and Optical microscope to study the various surface parameters such as Average roughness (Ra), Root mean square value (rms) and Peak value (PV) of the thrust surface.

The engineering of carrier dynamics in the MQW active region by modifying the p-type layers in the III-nitride based visible LEDs is described in this dissertation. It was found that the holes are preferentially injected into the QW adjacent to the p-InxGa1-xN layer with lower Indium mole fraction. Enhanced hole transport with increasing Indium mole fraction in the p-InxGa1-xN:Mg layer has been shown by analyzing the EL spectra. The improved hole transport and corresponding uniform distribution was achieved presumably by the potential barrier near the p-type layer and the MQW active region resulting in a modified kinetic energy of holes which creates a hole-transport-favorable environment in the MQW active region. At the same time, the limited hole injection due to the potential barrier for holes can be overcome under high injection conditions. The InAlN layers are widely used as an alternative high quality electron blocking layer in InGaN/GaN based visible LED structures. However, the Ga auto-incorporation of the InAlN layers has been recently reported during the growth of epitaxial layers by both MOCVD and MBE. The possible origins and a mechanism of Ga auto-incorporation of InAlN epitaxial layers were systematically investigated in this dissertation. It was found that the Ga-containing deposition on a wafer susceptor/carrier is the most dominant precursor for Ga auto-incorporation and the deposition on surrounding surfaces of quartz parts in a growth chamber is the other dominant source, while the effect of stainless-steel parts and interdiffusion of Ga atom from GaN underlayer are not critical. In addition, Mg or Cp2Mg in the growth chamber during InAl(Ga)N layer growth facilitates the auto-incorporation of Ga by modifying deposition conditions of GaN on the surrounding surfaces and the wafer susceptor/carrier. Based on experimental data of various cases, the Ga-containing deposition on any hot surfaces, which are also exposed to Indium precursor to form a liquid phase, is believed to be major origins of Ga auto-incorporation. In an effort to enhance the light extraction efficiency (LEE) in the LEDs, the direct patterning on the top surface of a LED structure, using laser interference ablation technique, has been studied in this dissertation. The 2-dimensional hexagonal lattice array of surface patterns was generated by direct irradiation of the laser source which is the interference of three laser beams onto the top p-GaN surface, without deterioration of electrical property of p-type layer and optical properties of MQW active region. The experimental results showed approximately 20 % improved LEE of the laser-patterned LED structure compared to the conventional LED structure without surface textures. Furthermore, the theoretical calculation using Monte-Carlo ray-tracing simulation confirmed the enhancement of LEE of the laser-patterned LED structure.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.

Xylan is one of the major hemicelluloses present in plant cell wall matrix, where it is closely associated with other cell wall components, cellulose and lignin. Xylan has enormous potential as a renewable biopolymer and recently, research in the direction of isolation and utilization of xylan is gaining lot of research attention. Extraction of xylan from the plant cell walls involves the hydrolysis of xylan and its transfer from the plant cell wall matrix to the hydrolyzing media. Current process of extraction involves prolonged heating of the biomass with the hydrolysis media at high temperature and/or pressure that leads to molecular degradation of xylan and limits its high potential polymeric applications. In this research, microwave assisted alkaline extraction of polymeric xylan from birch wood is investigated as an alternative to the time intensive conventional extraction. The hypothesis to be tested is that the microwave’s selective heating ability leads to the generation of hot spots through its interaction with the alkali present in the fibers and the resulting "explosion effect" loosen the recalcitrant fiber structure network thereby facilitating the hydrolysis of xylan and its dissolution before undergoing significant degradation. Effect of microwave extraction on the yield of xylan and wood solubilization, physico-chemical properties of wood fibers and of isolated xylan were investigated in comparison with conventional extraction. Low power input microwave (110 W) alkaline extraction was found to be an efficient alternative to the conventional extraction. FTIR and chemical composition of wood fibers after extraction demonstrated an increased removal of xylan from the wood fibre using microwave extraction. SEM, X-ray microtomography, and X-ray crystallinity studies of wood fibers demonstrated a porous and loosened fibre structure after microwave extraction confirming the hypothesis. Molecular weight of the isolated xylan using microwave extraction was found to be higher compared to the xylan isolated using conventional extraction indicating less molecular degradation. About 75% of xylan present in birch wood could be extracted using a low power input microwave heating under optimized extraction conditions of 8wt% NaOH solution, 1:8 (g:mL) solid to liquid ratio, and 25 minutes of extraction time.