A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.

A new class of polymer stabilized gadolinium trifluoride nanoparticles (NPs) have been developed as contrast agents for magnetic resonance imaging (MRI) and computed tomography (CT), with potential long term goals in targeted imaging and anti-cancer therapy. The NPs are comprised of a 90/10 mixture of GdF3/EuF3 and are coated with linear polyacrylic acid (PAA) chains consisting of 25 repeating units. The resulting aggregates are stable in serum and possess unprecedented mass relaxivities [i.e. ~100-200 s-1(mg/mL)-1]. Electron microscopy images reveal various NP morphologies which depend on the exact synthesis protocol. These include highly cross-linked oblong clusters with 30-70 nm cross sections, extensively cross-linked aggregates with 100-300 nm cross sections, and distinct polymer stabilized nanocrystals with 50 nm diameters. Their application as contrast agents in T1-weighted MRI studies, CT imaging at various X-ray energies, and preliminary rat brain perfusion studies was also tested. NP contrast enhancement was compared to Gd-DPTA (Magnevist®) and iopramide (Ultravist 300®) to demonstrate their high contrasting properties and potential as multimodal contrast agents.

Marine biofouling is the accumulation of marine species on surfaces submerged in seawater leading to unwanted problems for man-made surfaces such as hulls of ships and aquaculture nets. Historically, the amount of biofouling was regulated using metal based coatings whose usage have been disused lately due to adverse toxic effects. Alternative environmentally friendly coatings are currently avidly being pursued. Nanopatterned polymer thin films were investigated as potential candidates for marine antifouling coatings. Polystyrene-block-poly(2-vinyl pyridine) and polystyrene-block-poly(methyl methacrylate) diblock copolymer thin films self-assembled using vapor solvent annealing into cylinders perpendicular to the substrate composed of poly(2-vinyl pyridine) or poly(methyl methacrylate) respectively with diameters between 30 nm to 82 nm and center-to-center spacing between 46 nm to 113 nm in a polystyrene matrix on various substrates such as silicon or nylon. Polystyrene-block-poly(2-vinyl pyridine) copolymers were also mixed with the photoinitiator benzophenone and irradiated with ultraviolet light to crosslink the polymer chains and decrease the surface hydrophobicity. In the case of polystyrene-block-poly(methyl methacrylate), the yield of these nanopatterned films increased with the modification of the vapor annealing method. A low temperature vapor annealing technique was developed in which the annealing occurs at 2 °C. In another strategy, polystyrene and poly(2-vinyl pyridine) homopolymers were nanopatterned with alternating lines and grooves with widths between 200 nm and 900 nm and depths between 15 nm to 100 nm using Thermal Nanoimprint Lithography. Poly(2-vinyl pyridine) films were synthesized as brushes using surface initiated Atom Transfer Radical Polymerization to produce robust polymer films. The chemical and/or the topographical heterogeneity of the polymer surfaces influenced the settlement of Ulva linza algae zoospores. Overall, the incorporation of nanoscale features enhanced the antifouling properties of the samples. Further exploration of these types of coatings is highly encouraged.

Marine biofouling is the accumulation of marine species on surfaces submerged in seawater leading to unwanted problems for man-made surfaces such as hulls of ships and aquaculture nets. Historically, the amount of biofouling was regulated using metal based coatings whose usage have been disused lately due to adverse toxic effects. Alternative environmentally friendly coatings are currently avidly being pursued. Nanopatterned polymer thin films were investigated as potential candidates for marine antifouling coatings. Polystyrene-block-poly(2-vinyl pyridine) and polystyrene-block-poly(methyl methacrylate) diblock copolymer thin films self-assembled using vapor solvent annealing into cylinders perpendicular to the substrate composed of poly(2-vinyl pyridine) or poly(methyl methacrylate) respectively with diameters between 30 nm to 82 nm and center-to-center spacing between 46 nm to 113 nm in a polystyrene matrix on various substrates such as silicon or nylon. Polystyrene-block-poly(2-vinyl pyridine) copolymers were also mixed with the photoinitiator benzophenone and irradiated with ultraviolet light to crosslink the polymer chains and decrease the surface hydrophobicity. In the case of polystyrene-block-poly(methyl methacrylate), the yield of these nanopatterned films increased with the modification of the vapor annealing method. A low temperature vapor annealing technique was developed in which the annealing occurs at 2 °C. In another strategy, polystyrene and poly(2-vinyl pyridine) homopolymers were nanopatterned with alternating lines and grooves with widths between 200 nm and 900 nm and depths between 15 nm to 100 nm using Thermal Nanoimprint Lithography. Poly(2-vinyl pyridine) films were synthesized as brushes using surface initiated Atom Transfer Radical Polymerization to produce robust polymer films. The chemical and/or the topographical heterogeneity of the polymer surfaces influenced the settlement of Ulva linza algae zoospores. Overall, the incorporation of nanoscale features enhanced the antifouling properties of the samples. Further exploration of these types of coatings is highly encouraged.

The emerging field of nanotechnology, which spans diverse areas such as nanoelectronics, medicine, chemical and pharmaceutical industries, biotechnology and computation, focuses on the development of devices whose improved performance is based on the utilization of self-assembled nanoscale components exhibiting unique properties owing to their miniaturized dimensions. The first phase in the conception of such multifunctional devices based on integrated technologies requires the study of basic principles behind the functional mechanism of nanoscale components, which could originate from individual nanoobjects or result as a collective behaviour of miniaturized unit structures. The comprehensive studies presented in this thesis encompass the mechanical, dynamical and photophysical aspects of three nanoscale systems. A newly developed europium sulfide nanocrystalline material is introduced. Advances in synthetic methods allowed for shape control of surface-functionalized EuS nanocrystals and the fabrication of multifunctional EuS-CdSe hybrid particles, whose unique structural and optical properties hold promise as useful attributes of integrated materials in developing technologies. A comprehensive study based on a new class of multifunctional nanomaterials, derived from the basic unit of barcoded metal nanorods is presented. Their chemical composition affords them the ability to undergo autonomous motion in the presence of a suitable fuel. The nature of their chemically powered self-propulsion locomotion was investigated, and plausible mechanisms for various motility modes were presented. Furthermore functionalization of striped metallic nanorods has been realized through the incorporation of chemically controlled flexible hinges displaying bendable properties. The structural aspect of the light harvesting machinery of a photosynthetic cryptophyte alga, Rhodomonas CS24, and the mobility of the antenna protein, PE545, in vivo were investigated. Information obtained through a combination of steady-state and time-resolved spectroscopy in conjunction with quantum chemical calculations aided in the elucidation of the dynamics and the mechanism of light harvesting in the multichromophoric phycobiliprotein phycocyanin PC645 in vitro. Investigation of the light-harvesting efficiency and optimization of energy transfer with respect to the structural organization of light-harvesting chromophores on the nanoscale, can provide us with fundamental information necessary for the development of synthetic light-harvesting devices capable of mimicking the efficiency of the natural system.

Apertureless near-field scanning infrared microscopy is a technique in which an impinging infrared beam is scattered by a sharp atomic force microscopy (AFM) tip oscillating at the resonant frequency of the cantilever in close proximity to a sample. Several advantages offered by near-field imaging include nanoscale imaging with high spatial resolution (near-field imaging is not restricted by the diffraction limit of light) and the ability to differentiate between chemical properties of distinct compounds present in the sample under study due to differences in the scattered field. An overview of the assembly, tuning, and implementation of the near-field instrumentation is provided, as well as detailed descriptions about the samples probed and other instrumentation used. A description of the near-field phenomena, a comparison between aperture and apertureless-type near-field microscopy, and the coupled dipoles model explaining the origin of the chemical contrast present in near-field infrared imaging was discussed. Simultaneous topographic and chemical contrast images were collected at different wavelengths for the block copolymer thin film, polystyrene-b-poly(methyl ethacrylate) (PS-b-PMMA) and for amyloid fibrils synthesized from the #21-31 peptide of β2-microglobulin. In both cases it was observed that the experimental scattered field spectrum correlates strongly with that calculated using the far-field absorption spectrum, and using near-field microscopy, nanoscale structural and/or compositional variations were observed, which would not have been possible using ensemble FTIR measurements. Lastly, tip-enhanced Raman spectra of the #21-31 and #16-22 peptide fragments from the β2-microglobulin and Aβ(1-40) peptide were collected, examined, and an outline of the optimization conditions described.

Several nanomaterials systems, both inorganic and organic in nature, have been extensively investigated by a number of characterization techniques including atomic force microscopy (AFM), electron microscopy, Fourier transform infrared spectroscopy (FTIR), and energy dispersive x-ray spectroscopy (EDX). The first system consists of boron nitride nanotubes (BNNTs) synthesized via two different methods. The first method, silica-assisted catalytic chemical vapour deposition (SA-CVD), produced boron nitride nanotubes with different morphologies depending on the synthesis temperature. The second method, growth vapour trapping chemical vapour deposition (GVT-CVD), produced multiwall boron nitride nanotubes (MWBNNTs). The bending modulus of individual MWBNNTs was determined using an AFM three-point bending technique, and was found to be diameter-dependent due to the presence of shear effects. The second type of nanomaterial investigated is the biomineralized calcareous shell of the serpulid Hydroides dianthus. This material was found to be an inorganic-organic composite material composed of two different morphologies of CaCO3, collagen, and carboxylated and sulphated polysaccharides. The organic components were demonstrated to mediate the mineralization of CaCO3 in vitro. The final system studied is the proteinaceous cement of the barnacle Amphibalanus amphitrite. The secondary structure of the protein components was investigated via FTIR, revealing the presence of β-sheet conformation, and nanoscale rod-shaped structures within the cement were identified as β-sheet containing amyloid fibrils via chemical staining. These rod-shaped structures exhibited a stiffer nature compared with other structures in the adhesive, as measured by AFM nanoindentation.

A new class of polymer stabilized gadolinium trifluoride nanoparticles (NPs) have been developed as contrast agents for magnetic resonance imaging (MRI) and computed tomography (CT), with potential long term goals in targeted imaging and anti-cancer therapy. The NPs are comprised of a 90/10 mixture of GdF3/EuF3 and are coated with linear polyacrylic acid (PAA) chains consisting of 25 repeating units. The resulting aggregates are stable in serum and possess unprecedented mass relaxivities [i.e. ~100-200 s-1(mg/mL)-1]. Electron microscopy images reveal various NP morphologies which depend on the exact synthesis protocol. These include highly cross-linked oblong clusters with 30-70 nm cross sections, extensively cross-linked aggregates with 100-300 nm cross sections, and distinct polymer stabilized nanocrystals with 50 nm diameters. Their application as contrast agents in T1-weighted MRI studies, CT imaging at various X-ray energies, and preliminary rat brain perfusion studies was also tested. NP contrast enhancement was compared to Gd-DPTA (Magnevist®) and iopramide (Ultravist 300®) to demonstrate their high contrasting properties and potential as multimodal contrast agents.