This dissertation describes the development of a new method for increasing the resolution of the current protein microarray technology, down to the single molecule detection level. By using a technique called size-dependent self-assembly, different proteins can be bound to different sized fluorescent nanostructures, and then located on a patterned silicon substrate based on the sized pattern which is closest to the size of the bead diameter.The protein nanoarray was used to detect antibody-antigen binding, specifically anti-mouse IgG binding to mouse IgG. The protein nanoarray is designed with the goal of analyzing rare proteins. However, common proteins, such as IgG, are used in the initial testing of the array functionality. Mouse IgG, representing rare proteins, is conjugated to fluorescent beads and the beads are immobilized on a patterned silicon surface. Then anti-mouse IgG binds to the mouse IgG on the immobilized beads. The binding of the antibody, anti-mouse IgG, to the antigen, mouse IgG is determined by fluorescent signal attenuation.The first objective was to bind charged nanoparticles, conjugated with proteins, to an oppositely charged silicon substrate. Binding of negatively charged gold nanoparticles (AuNP), conjugated with mouse IgG, to a positively charged silicon surface was successful.The second objective was to demonstrate the method of size-dependent self-assembly at the nanometer scale (<100 >nm). Different-sized, carboxylated, fluorescent beads and AuNP, which were conjugated with proteins, were serially added to a patterned polymethyl methacrylate (PMMA) coated silicon surface. Size-dependent self-assembly was successfully demonstrated, down to the nanometer scale.The final objective was to obtain a signal from antibody-antigen binding within the protein array. Conjugated fluorescent beads were bound to e-beam patterns and signal attenuation was measured when the antibodies bound to the conjugated beads. The size-dependent self-assembly is a valuable new method that can be used for the detection and quantification of proteins.

No description available.

This thesis is focused on the fabrication and characterization of self-assembled arrays of magnetic iron oxide (Fe3O4, γ-Fe2O3 and Fe1-xO) nanoparticles. The synthesis of spherical and cubic iron oxide nanocrystals, with sizes between 5 and 30 nm and narrow size distributions, is demonstrated, along with a rigorous morphological characterization of the cubic nanoparticles. The transformation of core|shell Fe1-xO|Fe3-δO4 particles into single-phase Fe3-δO4 particles is studied in detail. It is found that anti-phase boundaries in the particles result in the emergence of anomalous magnetic properties i.e. exchange bias, and a reduced saturation magnetization compared to that of bulk Fe3O4. Cubic nanocrystals are assembled into arrays possessing an exceptionally high degree of translational ordering and a high degree of crystallographic alignment. A combination of electron microscopy and small-angle X-ray scattering is used in the characterization of the 3D nanostructures. The directional (anisotropic) interactions in the 3D structures are modeled in an attempt to find a link between the nanocrystal morphology and the corresponding mesostructure. Here, the cohesive van der Waals energy is estimated for a system of nanocubes with a variable truncation. The assembly of nanocubes in magnetic fields of various strengths is systematically investigated. A perturbed mesocrystal growth habit is observed at intermediate fields, whereas at high field strengths, the assembly is dominated by ferrohydrodynamic instabilities. Last, magnetometry is used to study the collective magnetic properties of self-assembled nanocrystals. The magnetic susceptibility in a weak magnetic field is studied as a function of film thickness and particle size. An increase in the tendency to form ferromagnetic couplings  with decreasing film thickness can be established. This 2D to 3D crossover of the magnetic properties of the nanoparticle arrays can be related to a change in the magnetic vortex states.

The practical applications of surfactant solutions in confined geometries require a thorough understanding of the system properties. Coarse-grained simulation techniques are useful for studying the qualitative behaviour of these systems, whereas the atomistic molecular dynamics (MD) technique can be used to obtain a molecular-level description. In this work, canonical MD simulations were performed using GROMACS version 4.0 to investigate the self-assembling behaviour of sodium octanoate (SO) confined between two parallel walls. In particular, the effects of gap size, wall type, and surfactant concentrations on the morphology of the surfactant aggregates were studied to gain in-depth knowledge of the system. The simulation results reveal that the morphology of the micelles formed between two parallel walls are affected not only by the gap size and surfactant concentration, but also by the nature and characteristics of the confining walls. With the graphite walls, most octanoate molecules are adsorbed at lower concentrations, but they form micellar aggregates as the surfactant concentration increases. Spherical micelles were found in the larger gaps (4 nm and 5 nm) but not in the smaller gap (3 nm), and the micellar shape also changes with increasing surfactant concentration. SO forms bilayer structures instead of spherical micelles between two silica walls. Interestingly, in the hydrophilic silica confinement, the orientation of these bilayers changes with gap sizes, whereas in the hydrophobic silica confinement, these bilayers remain perpendicular to the wall in all cases. Potentials of mean force between different molecules and atomic groups were determined under different conditions in order to develop a better understanding of the simulation results. It reveals, the presence of the confinement can alter the intermolecular interactions among the surfactant molecules, which, in turn, directly affects the self-assembling process, particularly the size and shape of the aggregates. Indeed, the formation of bilayers in silica wall confinement, as opposed to spherical micelles in graphite confinement, is caused by the enhanced electrostatic interactions between the charged atoms in the solution. The results of this study are expected to provide further insight into the self-assembling behaviour of confined surfactant systems, and may ultimately lead to the development of novel nanomaterials.

This Ph.D. thesis reports the discovery and study of several morphologies of ABC triblock copolymer assemblies in block selective solvents. One block copolymer self-assembled into helices (mostly double and some triple helices), and the other block copolymer formed a mixture of structures resembling hamburgers and striped cylinders. The helices, biomimmetic structures which are unusual from block copolymer self assembly, were prepared from the triblock copolymer poly(n-butyl methacrylate)-block-poly(2-cinnamoyloxyethyl methacrylate)-block-poly(tert-butyl acrylate) (PBMA-b-PCEMA-b-PtBA). They were formed spontaneously in several binary solvent mixtures including dichloromethane/methanol, tetrahydrofuran (THF)/methanol, and chloroform/methanol. They were formed in the composition ranges where the mixtures were good for the PtBA block, poor for the PCEMA block, and marginal for the PBMA block. The structure was studied and established by TEM, AFM, DLS and 1H NMR and by TEM tomography. The mechanism and kinetics of helix formation was examined. The Hamburger and striped cylinder structures were produced from poly(tert-butyl acrylate)-block-poly(2-cinnamoyloxyethyl methacrylate)-block-poly(succinated glyceryl monomethacrylate) or (PtBA-b-PCEMA-b-PSGMA) in mixtures of THF, (-)-sparteine and 1- or 2-propanol. Here THF solubilized all the blocks of the copolymer, while propanol was a precipitant for the middle block (PCEMA), and the chiral amine, (-)-sparteine, complexed with PSGMA and made it insoluble. Within the Hamburger-like structure, the “filling” was made of the complexed PSGMA chains and the "buns" were made of PCEMA. The striped cylinders were made of stacking alternating PCEMA and PtBA stubs. The PtBA chains were located on the outer surfaces of both of these structures. With the hamburger structures, after PCEMA crosslinking, we were able to remove the chiral amine by dialysis and make the PSGMA chains soluble again in solvents such as N, N dimethylformamide. The hamburgers were thus separated into two halves, with each half existing as a Janus particle, which had PtBA chains on one side and PSGMA chains on the other side. The Janus particles might have interesting applications, such as in Pickering emulsion stabilization. / Thesis (Ph.D, Chemistry) -- Queen's University, 2010-04-30 18:01:06.281

In this PhD thesis, the preparation of several types of hybrid materials of block copolymer and magnetic nanoparticles is described. The diversified morphologies of nanoaggregates formed by dispersing poly(glyceryl methacrylate)-block-poly(2-cinnamoyloxyethyl methacrylate)-block-poly(tert-butyl acrylate) tri-block copolymers in block selective solvents will be reported first. The volume occupied by the core block in these nanoaggregates can be swollen by solvent, and the core block can be sculpted. The cores can act potentially as the template to grow magnetic nanoparticles. Thus, a potential method for preparing hybrid magnetic materials of block copolymers and magnetic nanoparticles with different morphologies is developed. A one-pot method to synthesize cobalt nanoparticles covered by a polymer shell is then reported. This is achieved by thermally decomposing dicobalt octacarbonyl in the presence of polymeric multi-dentate ligand poly(ethylene glycol)-block-poly(acrylic acid). Using a similar method, cobalt nanoparticles covered by poly(2-cinnamoyloxyethyl methacryate)-block-poly(acrylic acid) ligand are synthesized. The cobalt nanoparticles fuse into chains for their magnetic dipole-dipole interaction. The chains are then coated with poly(tert-butyl acrylate)-block-poly(2-cinnamoyloxyethyl methacrylate). The coated Co chains are further locked by photo-crosslinking the poly(2-cinnamoyloxyethyl methacrylate) segments. The as-prepared cobalt nano wires have interesting magnetic response and may be used to build complicated magnetic nano devices. Another hybrid magnetic material is prepared via an oil-in-water emulsion method. The oil phase of the emulsion sphere consists of r-Fe2O3 magnetic nanoparticles covered with the poly(2-cinnamoyloxyethyl methacryate)-block-poly(acrylic acid) ligand and a poly(2-cinnamoyloxyethyl methacryate) homopolymer. It was dispersed in water using a mixture of poly(2-cinnamoyloxyethyl methacrylate)-block-poly(succinoylglyceryl methacrylate) and poly(2-cinnamoyloxyethyl methacrylate)-block-poly(glyceryl methacrylate) as the surfactants. The evaporation of the organic solvent left behind solid particles in water. The polymer chains on the surface of the obtained spheres allow the immobilization of biomolecules. Factors affecting the emulsion process are studied systematically. The emulsion spheres are characterized using TEM, AFM, TGA and etc. The emulsion sphere have potential application is immunoassay. The protein binding capacity of the spheres is determined. / Thesis (Ph.D, Chemistry) -- Queen's University, 2010-09-10 11:50:46.618

This thesis describes the examination of novel block copolymers that contain Ru(bpy)32+ complexes incorporated into one block of diblock copolymers made by ROMP. With the intent of exploring the potential usefulness of these interesting materials in applications such as light-harvesting and sensing, a systematic study of the solution self-assembly, luminescence properties, and the ability of the metal complex to engage in electron and energy transfer reactions has been conducted. / The solution self-assembly of block copolymers that contain Ru(bpy) 32+ complexes was examined first. Using a series of these block copolymers, a detailed study of the effects of block length, block ratio, polymer concentration and solution conditions on the copolymer self-assembly is presented. Using TEM, a number of morphologies were reproducibly observed including star micelles, large compound micelles, tubules, and interestingly, vesicles. These structures all contain the metal complex Ru(bpy)3 2+ within their core domains. / The luminescence properties of two block copolymers containing Ru(bpy) 32+ were examined: one polymer self-assembled into star micelles, the other into vesicles. Comparison of the unassembled polymer chains and the self-assembled polymers indicated that self-assembly, and confinement of the Ru(bpy)32+ complexes into the core domains of the aggregates, did not seriously adversely affect the luminescence properties of the metal complex. Measurement of the luminescence lifetime decay of the polymers suggested that energy migration occurred among the metal complexes along the polymer chain. The ability of the metal complexes within self-assembled structures to participate in electron transfer reactions with small molecules was also explored. It was found that from within the core domains of self-assembled structures, the Ru(bpy)32+ complexes could still engage in electron transfer reactions with molecules on the outsides or the insides of the aggregates, likely a result of energy migration. / The ability of Ru(bpy)32+ complexes within the cores of micelles to participate in energy transfer was explored. Micelles were formed in aqueous solutions using polymers that possessed both the metal complex and a water-soluble block. Several methods were attempted to encapsulate two molecules, a derivative of coumarin 2 and an Os(bpy)3 2+-based molecule, inside these micelles. It was observed that Ru(bpy) 32+ could act as an energy acceptor from the coumarin derivative, and could act as an energy donor to the osmium-based complex. Encapsulation of the small molecules greatly enhanced the efficiency of energy transfer, by non-covalently bringing the small molecules in close proximity to the Ru(bpy)32+ complexes. / Polymers were synthesized that contained a Ru(bpy)3 2+-based block and were terminated with the molecular recognition unit biotin. These polymers, upon self-assembly, formed micelles with biotin groups on their periphery. The addition of the protein streptavidin, which has a strong binding affinity for biotin, resulted in the aggregation of the self-assembled structures. This established the potential for self-assembled metal-containing aggregates to form higher-order structures. / Early work is presented in Appendix A involving block copolymers that contain hydrogen-bonding groups. Several methods were attempted to elucidate the solution morphologies of these polymers, namely IR, 1H NMR, DLS, and pyrene fluorescence. The transition of this initial work to polymers that contain the Ru(bpy)32+ complex is also described.

This dissertation mainly addresses the synthesis of well-ordered mesoporous titania thin films by dip coating with PEO-PPO-PEO triblock copolymer surfactant template P123. Because P123 is composed of poly(ethylene oxide) [PEO] and poly(propylene oxide) [PPO] blocks, concentrations of ingredients are adjusted to tune the films’ wall thickness, pore size and mesophase. Structural changes are consistent with partitioning of species among PEO blocks, PPO blocks, and the PEO/PPO interface. Titanates localize near PEO and increase wall thickness (by 5 nm to 7 nm). Depending on aging temperature, PPG either swells the PPO cores (when it is hydrophobic) or introduces large (>200 nm) voids (when it is hydrophilic but phase separates during heating). 1-butanol localizes at the PEO/PPO interface to favor a 3D hexagonal mesostructure. In another approach, anodizing Ti foils yields vertically aligned titania nanotubes arrays with exceptional stabilities as anodes in lithium ion batteries; they maintain capacities of 130-230 mAhg-1 over 200 cycles. No microstructural changes are induced by battery cycling and good electrical contact is maintained. A diffusion induced stress model suggests that thin-walled nanotubes arrays should be stable under testing conditions, and that ordered hexagonal columnar pore arrays should have both high charge/discharge rates and low stress development.

Loline alkaloids (LA) are secondary metabolites produced by Epichloandamp;euml; (anamorph, Neotyphodium) grass endophytes. They are toxic and deterrent to a broad range of herbivorous insects but not to livestock. This protective bioactivity has spurred considerable research into the LA biosynthetic pathway. LOL, the gene cluster containing nine genes, is required for LA biosynthesis. The regulation of LOL genes during LA production in culture and in symbio is of interest. In this study, coordinate regulation between LOL gene expression and LA production level was investigated in both MM culture and symbiota. Results showed that expression of LOL genes in N. uncinatum MM culture were tightly correlated with each other (p andamp;lt; 0.0005), and all presented a significant temporal quadratic pattern during LA production. Gene expression started before LA were detectable, and increased while LA accumulated. The highest gene expression level was reached before the highest amounts of LA were detected, and gene expression level declined to a very low level after amounts of LA plateaued. Observations suggested that the hierarchical clusters based on the correlation coefficient could help to predict the roles of LOL genes in the LA pathway. In symbiota, coordinate coregulation of LOL gene expression with LA was found in E. festucae-meadow fescue inflorescences and stromata, whereby lower LOL gene expression corresponded with the lower LA level in stromata. In N. uncinatum (or N. siegelii)-meadow fescue vegetative tissues, dramatically higher LA levels were found in younger leaf tissue than in older leaf tissue, yet no evidence was found to relate this difference to LOL gene expression differences. Instead, substrate availability may regulate the LA level. In particular, asparagine was more than 10-fold higher in young leaf tissue than in old tissue, although proline was significantly lower in young tissue. Therefore, different regulatory mechanisms underlie LOL gene expression and LA production in different circumstances. The GUS activity of Pro-lolC2-GUS and Pro-lolA2-GUS in Neotyphodium species was almost undetectable in culture, though the activity could be detected in symbiota. The mRNA of GUS did not exhibit the same pattern as lolC2 or lolA2 in culture during LA production time course. A Pro-lolC2-cre transgene was expressed in complex medium, in which lolC2 mRNA was not detectable. These results suggest that proper regulation of LOL genes in culture or symbiota is dependent on the LOL cluster.

Graphene is a two-dimensional sp2 hybridized carbon lattice that is also the fundamental building block of graphite. Graphene has attracted significant interest recently due to its distinctive electrical, optical and mechanical properties. These properties have spurred research directed at modifying graphene for use in a variety of electronic, optoelectronic, and sensor technologies. However, before graphene can be used in products, it is necessary to find methods to tune, modify, grow and integrate graphene features while substantially boosting device performance and maintaining current processing compatibility and ease of integration with existing manufacturing infrastructure. This dissertation focuses on developing techniques for controllably doping the graphene layer through scalable, industry friendly and simple chemical doping; using self-assembled monolayer compounds, photo-acid and photo-base generators, polymers and metal-organic species. We have, in fact, demonstrated simple p-n junctions fabricated in this manner. Characteristic I-V curves indicate the superposition of two separate Dirac points from the p and n regions, confirming an energy separation of neutrality points within the complementary regions; Raman studies of these methods have shown that these processes result in extremely low defect levels in the graphene. Our simple methods for producing patterned doping profiles in graphene films and devices open up a variety of new possibilities for forming complex doping profiles in a simple manner in graphene. This work can enable rapid testing, such as controlled work function tuning, complex doping profiles and simple post-fabrication tuning, of concepts for graphene that may be useful in both interconnect and transparent conductor applications. In addition to graphene doping, we also investigated approaches to the synthesis of few-layer graphene flakes, since current techniques still produce inferior materials. Exfoliation of Graphene Sheets by an Electron Donor Surfactant was demonstrated to generate few-layers graphene flakes that rival the electrical quality of reduce graphene-oxide (rGO) flakes. Last but not least, Diels-Alder adducts on silica were explored as a controllable carbon precursor for pristine graphene; these allow for a rational direct-growth-of-graphene-on-surface reaction mediated by copper catalyst, without the use of flammable precursors, such as methane, that are used in current methods of chemical vapor deposition synthesis of graphene.