InAs/InP multiwavelength quantum dash lasers are promising solutions to rising data loads in our telecommunications systems, as one laser chip can replace many lasers operating at a single wavelength. Quantum dashes are quasi-one-dimensional nanoparticles that offer equal or increased performance as laser gain media when compared to equivalent quantum well devices. InAs/InP quantum dashes are ideal for laser devices emitting in the C-band region, centred around 1550 nm. The quantum dashes in this thesis are epitaxially grown via the self assembled Stranski-Krastanow mode. Characterizing how structure and composition of these quantum dashes affect the energy level spacing and emission wavelengths is crucial for designing better performing telecommunications lasers. In this thesis a method for determining the average heights and widths of these nanoparticles from atomic force microscopy measurements of uncapped InAs/InGaAsP/InP quantum dashes is developed. Single quantum dash simulations are built in Crosslight Photonic Integrated Circuit Simulator (PICS3D) with the lowest energy transition tuned to photoluminescence peak wavelengths provided by National Research Council Canada. These simulations are used to determine the impact of quantum dash dimensions, compositions, and heterostructure changes to the overlap integrals and emission energies. Phosphorus concentration within the quantum dash and wetting layer can modify the predicted emission wavelength by ∼200 nm, and increasing quantum dash lengths beyond 200 nm has negligible effect on emission energy and energy level spacing. The sublayer thickness is increased from 0.1 to 1 nm, and shows that emission energy will increase for GaP sublayers and decrease for GaAs sublayers by up to 30 meV. The role of the wetting layer on energy level spacing is discussed and determined to increase the emission energy by ∼15 meV when the 0.5 nm wetting layer is removed for a 2 nm quantum dash. The role of As/P intermixing is investigated in three ways: by incorporating phosphorus concentration in (1) the quantum dash and wetting layer, (2) the wetting layer, and (3) the lower portion of the quantum dash without a wetting layer. There is negligible change in the overlap integral for these three cases with all other variables held constant, and the trends between each case remain the same. Further experimental analysis of buried InAs quantum dashes is recommended for compositional information. The implementation of variable strain profiles in this model is also recommended, in addition to developing vertically coupled quantum dash simulations. Finally, performing these simulations at varying temperatures will better represent the operating conditions of quantum dash lasers.

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There is a need for the development of new technologies for the early detection of disease. Diverse initiatives are underway in academia and the pharmaceutical and biotechnology industries to develop highly-sensitive, high-throughput methods to detect disease-relevant biomarkers at the single-cell level. Biomarkers can define the progress of a disease or efficacy of disease treatment, and can include nucleic acids (RNA, DNA), proteins, small molecules, or even specific cells. While discovery research in this area is accelerating, there are a number of current experimental limitations. Most existing methodologies require a relatively large sample size. Also, amplification-based detection technologies are destructive to sample, and errors in amplification can occur, leading to an incorrect diagnosis. Nanomaterial-based devices (nanodevices) offer the promise of label-free, amplification-free detection strategies. Such nanodevices could allow analysis of minute biological samples without the requirement for amplification or incorporation of reporter groups. Loss of sample, due to handling and processing would be minimized and the sample could be recovered for further analysis. Atomic force microscopy (AFM) allows topographic imaging and compressibility/elasticity measurement of biomolecules on solid supports. AFM can enable assays of ligand binding with single molecule detection capability. Certain nucleic acid types, in particular double-stranded (ds) RNA, can act as a biomarker for specific cancers (e.g. leukemia) and viral infection. dsRNA also is of interest since it is a conserved structural feature of precursors to gene-regulatory RNAs, including micro (mi) RNAs and short interfering (si) RNAs. This project demonstrates a single-step, label-free, amplification-free approach for detecting the interaction of biomolecules that bind and/or process dsRNA, using a nanomanipulated, self-assembled monolayer (SAM) of a ds[RNA-DNA] chimera as imprinting matrix, a reference nuclease as imprinting agent, and AFM for imprint-readout. The action of the dsRNA-specific enzyme, ribonuclease III (RNase III), as well as the binding of an inactive, dsRNA-binding RNase III mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA] chimera, as measured by atomic force microscopy, provides a distinct digital output for each type of input. These findings provide the basis for developing imprinting-based nano-biosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale. RNA-DNA heteroduplexes are biomarkers for specific inflammatory conditions of genetic origin, and also are the product of capture of an RNA (e.g., miRNA) by a complementary DNA sequence. The approach used here to detect RNA-DNA hybrids is based on the ability of alkylthiol-modified ssDNA molecules to form monolayers and nanomatrices on gold surfaces (as described above) with density-dependent thickness, which increases upon formation of RNA-DNA hybrids following addition of a complementary oligoribonucleotide. Changes in hybrid matrix thickness can be measured by AFM, using a reference monolayer. RNA-DNA hybrid formation as well as subsequent processing by RNase H can be observed as a height increase or decrease, respectively, of the monolayer. When Mg2+ is omitted to prevent RNA cleavage, but not protein binding, a significant height increase is observed. The height increase is not observed with the corresponding ssDNA or ssRNA nanomatrices, and only occurs with nanomatrices having a hybrid density above a defined threshold. The data indicate formation of a stable multimeric RNase H assembly on the hybrid nanomatrix which provides a robust signal that is nondestructive to the RNA. The implications of these findings are discussed with respect to development of novel detection methodologies for RNA, dsRNA, and RNA-DNA hybrids. / Chemistry

The heart, as a vital organ, must pump continuously to deliver oxygenated blood to the tissues of the body. The physical stress of pumping is supported by the extracellular matrix (ECM), a dynamic protein scaffold inside and around the heart. While a regulated ECM is required to maintain heart function, aberrant or excessive ECM remodelling, called fibrosis, is associated with disease states and is a hallmark of cardiovascular disease. One major trigger of cardiovascular disease is obesity, and fibrotic remodelling is known to occur in this context. In order to study the impact of increased body size on heart function and the molecular and biophysical characteristics of the ECM, a larval overgrowth model for obesity in the genetic model Drosophila melanogaster has been developed and characterised. This model produces giant larvae twice as heavy as their wildtype counterparts, and allows a unique opportunity to study changes in the cardiac ECM in a simple genetic model. Results demonstrate a remarkable ability of the ECM to accommodate this increase in size. The muscles of the heart are particularly robust, and there are no obvious observable defects to the matrix. Preliminary results suggest Collagen fibres are thicker and more disperse. When observing heart functionality, the cross-sectional area of the heart lumen is increased significantly in giant larvae, both at diastole and systole. However, giant larvae display defects in contraction of the heart tube, characterised by an inability to contract fully at systole. This results in a less than proportional increase in stroke volume, and an increase in heart rate. Heart function of giant larvae is clearly affected by the increase in body size. To quantify the impact to the biophysical structure of the ECM, an atomic force microscopy protocol is being developed. / Thesis / Master of Science (MSc) / A known side effect of cardiovascular disease is fibrosis of the heart, a form of pathological extracellular matrix (ECM) remodelling. Fibrosis causes the stiffening of heart muscle, leading to impaired cardiac function. One of the main risk factors for the development of cardiovascular disease is obesity, and fibrosis is known to occur in this context. I have characterised changes in the morphology and physiology of the heart in a Drosophila model for obesity. The resulting cardiac hypertrophy reveals significant plasticity in the heart ECM, while heart contraction and output is compromised.

Living systems possess seemingly bottomless complexity. Attempts to parse the details of one cellular process from all other concurrent processes are challenging, if not daunting undertakings. The apparent depth of this problem, as it pertains to biomineralization, is related to the small number of existing studies focused on the development of a mechanism-based understanding of intracellular mineralization processes. Molecular biologists and geneticists have only begun to turn their attention towards identification and characterization of molecules involved in regulating and controlling biomineral formation. With this new knowledge, a number of new and exciting research opportunities are currently awaiting development upon a barren landscape. Silica biomineralization is one of these emerging frontiers. As new information about the chemical and structural nature of the macromolecules involved in biosilicification is revealed, the means these species employ to control the temporal and spatial onset of silica deposition in vivo become available for exploration. The first chapter of this dissertation outlines those aspects of silicate metabolism that are directly relevant to the controlled biomineralization of silica in eukaryotic organisms and identifies pervasive and unanswered questions surrounding biosilica formation. Particular attention is paid to the diatoms, which are the most abundant, and extensively investigated silica-mineralizing organisms in modern seas. The extent, and mechanism through which specific organic moieties work individually or in concert to direct mineral formation at biological interfaces is a central concern of modern biomineralization research. Chapter two addresses this forefront issue for silica mineralizing systems, and reports the results of an experimental investigation designed to measure the effects of individual surface-bound organic functional groups on the rate of surface-directed silica nucleation. Chapter three discusses an additional aspect of this research aimed at investigating the reactivity of nanoparticulate biogenic silica produced by marine phytoplankton and terrestrial plants in natural environments. Density Functional Theory and ab initio molecular orbital calculations are employed to explore potential mechanisms underlying the catalytic activity of divalent metal cations during the hydrolysis of Si – O bonded networks. / Ph. D.

Central to tapping mode atomic force microscopy is an oscillating cantilever whose tip interacts with a sample surface. The tip-surface interactions are strongly nonlinear, rapidly changing, and hysteretic. We explore numerically a lumped-mass model that includes attractive, adhesive, and repulsive contributions as well as the interaction of the capillary fluid layers that cover both tip and sample in the ambient conditions common in experiment. To accomplish this, we have developed and used numerical techniques specifically tailored for discontinuous, nonlinear, and hysteretic dynamical systems. In particular, we use forward-time simulation with event handling and the numerical pseudo-arclength continuation of periodic solutions. We first use these numerical approaches to explore the nonlinear dynamics of the cantilever. We find the coexistence of three steady state oscillating solutions: (i) periodic with low-amplitude, (ii) periodic with high-amplitude, and (iii) high-periodic or irregular behavior. Furthermore, the branches of periodic solutions are found to end precisely where the cantilever comes into grazing contact with event surfaces in state space corresponding to the onset of capillary interactions and the onset of repulsive forces associated with surface contact. Also, the branches of periodic solutions are found to be separated by windows of irregular dynamics. These windows coexist with the periodic branches of solutions and exist beyond the termination of the periodic solution. We also explore the power dissipated through the interaction of the capillary fluid layers. The source of this dissipation is the hysteresis in the conservative capillary force interaction. We relate the power dissipation with the fraction of oscillations that break the fluid meniscus. Using forward-time simulation with event handling, this is done exactly and we explore the dissipated power over a range of experimentally relevant conditions. It is found that the dissipated power as a function of the equilibrium cantilever-surface separation has a characteristic shape that we directly relate to the cantilever dynamics. We also find that despite the highly irregular cantilever dynamics, the fraction of oscillations breaking the meniscus behaves in a fairly simple manner. We have also performed a large number of forward-time simulations over a wide range of initial conditions to approximate the basins of attraction of steady oscillating solutions. Overall, the simulations show a complex pattern of high and low amplitude periodic solutions over the range of initial conditions explored. We find that for large equilibrium separations, the basin of attraction is dominated by the low-amplitude periodic solution and for the small equilibrium separations by the high-amplitude periodic solution. / Ph. D.

The foundational studies of this dissertation concern the characterization of segmented polyurethanes and polyureas synthesized without the use of chain extenders'molecules that are typically used to promote a microphase separated morphology that gives these materials their useful characteristics. Polyurethanes in which a single asymmetric diisocyanate comprising the whole of the hard segment were found to display poor microphase separation. Conversely, polyurethanes in which a single symmetric diisocyanate composed the hard segment were found to display good microphase separation. The more efficient packing of the symmetric hard segments also led to an increase in hard segment connectivity and hence higher values of storage moduli in these systems. When hydroxyl-terminated diisocyanates were replaced with amine-terminated diisocyanates, polyureas were formed. Here too, diisocyanate symmetry was found to play a key role with symmetric diisocyanates leading to better microphase separation. In addition, the polyurea materials displayed broader service temperature windows than their polyurethane counterparts as the relatively stronger bidentate hydrogen bonding replaced monodentate hydrogen bonding in these materials. A thread-like, microphase separated morphology was visually confirmed using atomic force microscopy. Other techniques such as ambient temperature tensile testing, and wide and small angle x-ray scattering were employed to confirm the presence of the microphase separated structure. The investigation into the effects of diisocyanate chemistry and its symmetry was broadened to incorporate non-chain extended polyurethane materials with different soft segment molecular weights, as well as polyurethanes that did contain chain extenders. Once again the effect of using symmetric versus asymmetric diisocyanates was evident in the structure–property behavior of these systems, with symmetric diisocyanates forming materials that displayed better microphase separation and more connectivity of their hard domains. Lastly, in a departure from the segmented copolymer area, a study was conducted into the influence of casting variables on the solid-state structure of synthetic polypeptide films based on glutamate chemistry. The effect of solvent evaporation was determined to play a key role in the morphology of these polypeptide films. Measured small angle light scattering patterns were compared to computer calculated patterns to reveal information about the structure, shape, and length scale of the polypeptide structure. / Ph. D.

Micro and nanoscale systems are rapidly evolving to improve the resolution of experimental measurements. Experiments involving such small scale devices are difficult and expensive, and the available analytical theory to describe their dynamics is idealized. The dynamics of microscopic cantilevers in fluid are complicated and include significant contributions from many sources in an actual experiment. Some examples are: complex cantilever geometries, near-wall effects, thermal and external actuation techniques, and a variety of measurement techniques. Numerical simulations are a powerful approach to describe the dynamics of micro and nanoscale systems for the precise conditions of experiment. This thesis provides a numerical approach capable of addressing these inherent challenges and quantifies the dynamics of microscopic cantilevers in fluid for experimentally relevant conditions. A thermodynamic approach based upon the fluctuation-dissipation theorem allows for the calculation of stochastic dynamics from deterministic dynamics. Using numerical simulations, the thermal motion can be described for the precise conditions of experiment. It is found that the measured dynamics of cantilevers differs depending on the quantity being measured. In particular, the dynamics of displacement and angle of the cantilever tip distribute energy differently to the higher flexural modes. The externally driven dynamics of microscale cantilevers in fluid are also considered. The driven dynamics are calculated using numerical simulations of the cantilever response to a force impulse. It is found that the driven dynamics depend upon the type of actuation in addition to the quantity measured. A comparison of the driven dynamics to the corresponding stochastic dynamics yields insight into the nature of the Brownian force acting on the cantilever. Another experimentally relevant condition is the use of cantilevers with V-shaped planforms in fluid. The resulting flow field is three-dimensional and complex in contrast to what is found for a long and slender rectangular cantilever. Despite the flow complexity, the stochastic and driven dynamics of the fundamental mode can be predicted using a two-dimensional model with an appropriately chosen length scale. An experimentally motivated magnetomotive actuation technique is investigated. Results show that this approach generates power spectra nearly equivalent to the noise spectra. Furthermore, the case of a V-shaped cantilever in fluid and oscillating in proximity of a solid boundary is investigated. In the presence of a solid surface the fluid damping and added mass of fluid on the cantilever are larger than for a cantilever far from boundaries. This results in a lower frequency and quality factor for the fundamental resonance. This can impede experimental efforts because broad peaks lack distinct features that can be used to identify experimental signals. An option to overcome the large viscous damping is to take advantage of higher modes of cantilever oscillation. The higher frequency oscillations of the higher modes generate a smaller viscous boundary layer and have a reduced added mass. As a result, the quality factor increases with increasing mode number. The frequency dependence of the fluid dynamics around a fluctuating microscale cantilever is also studied. The mass of fluid entrained by the cantilever and the viscous damping quantify the interaction of a cantilever with the surrounding fluid and are computed. Analytical expressions for these parameters are derived for moderate mode number. The techniques and findings of this thesis have broad applicability to a wide range of micro and nanotechnologies that rely upon understanding the dynamics of small scale structures in fluid. / Ph. D.