abstract: DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops. / Dissertation/Thesis / Ph.D. Biochemistry 2013

Quantum dots are semiconductor nanocrystals that have tunable emission through changes in their size. Producing bright, efficient quantum dots with stable fluorescence is important for using them in applications in lighting, photovoltaics, and biological imaging. This study aimed to optimize the process for coating CdSe quantum dots (which are colloidally suspended in octadecene) with a ZnS shell through the pyrolysis of organometallic precursors to increase their fluorescence and stability. This process was optimized by determining the ZnS shell thickness between 0.53 and 5.47 monolayers and the Zn:S ratio in the precursor solution between 0.23:1 and 1.6:1 that maximized the relative photoluminescence quantum yield (PLQY) while maintaining a small size dispersion and minimizing the shift in the center wavelength (CWL) of the fluorescence curve. The process that was developed introduced a greater amount of control in the coating procedure than previously available at Cal Poly. Quantum yield was observed to increase with increasing shell thickness until 3 monolayers, after which quantum yield decreased and the likelihood of flocculation of the colloid increased. The quantum yield also increased with increasing Zn:S ratio, possibly indicating that zinc atoms may substitute for missing cadmium atoms at the CdSe surface. The full-width at half-maximum (FWHM) of the fluorescence spectrum did not change more than ±5 nm due to the coating process, indicating that a small size dispersion was maintained. The center wavelength (CWL) of the fluorescence spectrum red shifted less than 35 nm on average, with CWL shifts tending to decrease with increasing Zn:S ratio and larger CdSe particle size. The highest quantum yield was achieved by using a Zn:S ratio of 1.37:1 in the precursor solution and a ZnS shell thickness of approximately 3 monolayers, which had a red shift of less than 30 nm and a change in FWHM of ±3 nm. Photostability increased with ZnS coating as well. Intense UV irradiation over 12 hours caused dissolution of CdSe samples, while ZnS coated samples flocculated but remained fluorescent. Atomic absorption spectroscopy was investigated as a method for determining the thickness of the ZnS shell, and it was concluded that improved sample preparation techniques, such as further purification and complete removal of unreacted precursors, could make this testing method viable for obtaining quantitative results in conjunction with other methods. However, the ZnS coating process is subject to variations due to factors that were not controlled, such as slight variations in temperature, injection speed, and rate and degree of precursor decomposition, resulting in standard deviations in quantum yield of up to half of the mean and flocculation of some samples, indicating a need for as much process control as possible.

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<p>Silicon-based dielectric thin films including amorphous hydrogenated aluminium-doped silicon oxides (<em>a-</em>SiAl_xO_y:H), amorphous hydrogenated silicon nitrides (<em>a-</em>SiN_x:H), and amorphous hydrogenated silicon carbides (<em>a-</em>SiC_x:H) were deposited by remote plasma chemical vapour deposition (RPECVD) techniques including electron cyclotron resonance plasma enhanced chemical vapour deposition (ECR-PECVD) and inductively-coupled-plasma chemical vapour deposition (ICP-CVD) on silicon (Si) wafers, soda-lime glass microscope slides, and glassy carbon (C) plates. Aluminium (Al) in the SiAlO films was incorporated by way of a metalorganic Al(TMHD)₃ precursor.</p> <p>Thickness, refractive index, and growth rate of the films were measured using variable angle spectroscopic ellipsometry (VASE). Film composition was measured using energy dispersive X-ray spectroscopy (EDX) for the SiAlO films and Rutherford backscattering spectrometry (RBS) for the SiC_x films. Elastic modulus and hardness of the SiAlO and SiC_x films were measured using nanoindentation and their adhesion was characterized via progressive load scratch testing.</p> <p>All films were observed to be optically transparent at near-IR and red wavelengths with many SiN_x and SiC_x films exhibiting significant optical absorption above 2.25eV. Modification of a previously developed deposition recipe produced doubled growth rates in SiN_x and SiC_xfilms. SiAlO films were produced with up to 1.6±0.1at% aluninium (Al) incorporation, while SiC_x films with composition ranging from SiC_0.25:H to SiC₂:H could be produced depending on the growth gas flow ratios. SiAlO films exhibited hardness and reduced modulus (<em>H</em> and <em>E</em>) up to 8.2±0.4 and 75±2GPa, respectively; <em>H </em>and <em>E</em> for the SiC_xfilmsreached 11.9±0.2 and 87±3 GPa. Initially, adhesion to Si wafers was extremely poor with films delaminating at loads of 1.5±0.3N when scratched with a 3/16” alumina (Al₂O₃) sphere; implementation of a rigorous pre-deposition surface cleaning procedure produced films showing only cracking and no delamination up to 30N loads vs. a 200μm radius Rockwell C diamond stylus.</p> / Master of Applied Science (MASc)

Terahertz region in the electromagnetic spectrum is the region between Infrared and Microwave. As the Terahertz region has both wave and particle nature, it is difficult to make a room temperature, fast, and sensitive detector in this region. In this work, we fabricated a Palladium based IR detector and a CNT based THz bolometer. In Chapter 1, I give a brief introduction of the Terahertz region, the detectors already available in the market and different techniques I can use to test my detector. In Chapter 2, I explain about the Palladium IR bolometer, the fabrication technique I have used, and then we discuss the performance of the detector. In Chapter 3, I explained about the Roll to Roll based THz bolometer, its working and fabrication techniques, and at the end we discussed its performance.

Published Article / I n the context of government policy and international comparisons, the state of national nanoscience R&D is explored using bibliometric data as well as data sourced from the National Survey of Research and Experimental Development Inputs. This includes information about expenditure, ownership, collaboration and research fields. While the business sector performs the greatest proportion of nanotechnology R&D in South Africa, the higher education sector plays a critical role, and the science councils are common collaboration partners. In this context the development of catalysts and carbon nanotubes emerge as a key nanotechnology in South Africa.

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published_or_final_version / Mechanical Engineering / Doctoral / Doctor of Philosophy