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<p> This thesis summarizes theoretical results of two projects on the investigation of a novel organometallic polymer, the polyferrocenylsilanes(PFS). The study is carried out in collaboration with the experimental groups of Prof. Manners and Prof. Winnik at the Department of Chemistry of University of Toronto. </p> <p> In the first project, a rotational isomeric state (RIS) model is applied to study the configurational statistics of an ideal polyferrocenyldimethylsilane (PFDMS) chain: Fc[Fe(C5H4)2SiMe2]nH (Fe= Fe(C5H5)(C5H4)). The necessary conformation energies are derived from the molecular mechanics study of oligomeric (n=1,2) models for PFDMS reported by O'Hare et al.(J. Am. Chem. Soc. 1996, 118, 7578). In particular, pseudoatom and pseudobonds are introduced to describe the RIS chain of PFDMS, consistent with the special molecular geometry of the repeating ferrocene and organosilane units. The mean square unperturbed dimensions ((r^2)0, (R^2g)0), the characteristic ratios Cn(C∞) and the temperature coefficients dln (r^2)0/dT of PFDMS are calculated. The results show that an ideal PFDMS chain has a relatively low value of Coo and fast convergence of Cn to C∞ with increasing n, indicating a high static flexibility of this type of transition metal-containing polymer. The previously unknown Kuhn length of PFDMS is obtained based on the calculated C∞ </p> <p> In the second project, by taking PFS-b-PDMS/alkane as a model system, general phase behaviours of the self-assembled micelles in dilute crystalline-coil copolymer solutions (solvents are selective for the coil blocks) are investigated. Three types of aggregates - lamellar, rodlike and tubular micelles are studied based on the existing experimental observations. The computation results reveal three types of phase diagrams, namely, lamella-tube-rod phase diagrams with or without a triple point and lamella-rod phase diagrams. It is shown that lamella-tube-rod morphological transitions can be induced by changing the coil/crystalline block ratio or the temperature. Possible improvement of the theory and the current challenges of studying PFS-b-PDMS self-assembly in alkane solvents for both theories and experiments are discussed. </p> / Thesis / Master of Science (MSc)

This dissertation focuses on four research topics: self-assembly of colloidal nanoparticles, surface modifications of the properties of ionically self-assembled multilayer films, surface enhanced Raman spectroscopy of functionalized gold nanoparticles, and two photon uncaging in gel. Those techniques are used for development of novel nanofabrication methods for top-down and bottom-up assembly of nanostructures, by modifying the properties of nanopatterned surfaces with photoactive ligands, and other technologies. First I describe the development of an improved method for nanosphere lithography, a variation of the convective self-assembly technique. The method exhibited high reproducibility and yielded high quality monolayer crystals by withdrawing a meniscus of liquid polystyrene spheres solution and subsequent evaporation of the solvent. The monolayer crystal was used as an evaporation mask to create surface arrays of gold nanotriangular particles. Metal nanoparticles, with sharp features or narrow gaps, exhibit strong plasmonic properties. I took advantage of those properties to attempt to create patchy modifications of the surface functionalization of gold nanotriangular particles treated with photosensitive molecules. Two molecules denoted, P3-DTC, and LIP3, were used as functional molecules attached to the gold nanoparticles. After interaction with 356nm UV light, part of those molecules cleaves off the surface of the nanoparticles rendering the surface modified with a new functional group. The modification takes place only at the plasmonic hot spots of those nanoparticles, resulting in a patchy modification of the properties of the nanoparticles. I built polymer Ionically Self-assembled Multilayer (ISAM) films using a Layer-by-Layer deposition technique and treated them to alter their surface adhesion properties. Poly (allylamine hydrochloride) (PAH), and poly (styrene sulfonate) (PSS) are a very well-studied system of polyelectrolytes for LbL deposition. ISAM films built from those polyelectrolytes are rich in amine groups to which nanoparticles, cells, tissue cultures, ligands can be made to adhere. In my work I developed a method for selective modification of the surface adhesiveness, by neutralizing the amine groups trough acetylation with acetic anhydride. With resolution from a few microns to a few hundred nanometers, I selectively passivated some areas of the ISAM film while others I left unaltered. I tested the effect of the acetic anhydride passivation by performing Horse Radish Peroxidase (HRP) test which quantifies the amount of free amines on the surface of the film. I also demonstrated the patchy modification of surface adhesiveness by introducing gold nanospheres which attached only to the amine active areas of the modified ISAM film. Photoactivatable fluorophores, i.e. compounds and other entities that may transform into a fluorescent form on absorption of a photon can be employed in multidimetional volume patterning. I studied the photoactivation of aryl azides in gelatin matrix. Specifically, I used Azidocoumarin 151 as a test molecule to undergo two-photon activation, and then measured the resulting photoluminescence. The activation of the Azidocoumarin 151 can be used to create arbitrary 3D patterns of modified functionality inside the gel. The activated molecules can be used as sites for further modification of the patterning inside the volume of the gel. Possible modifications include attaching biomolecules, nanoparticles, or individual cells. / Ph. D.

No / Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8,000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.

No / Discovery of new catalysts for demanding aqueous reactions is challenging. Here, we describe methodology for selection of catalytic phages by taking advantage of localized assembly of the product of the catalytic reaction that is screened for. A phage display library covering 109 unique dodecapeptide sequences is incubated with nonassembling precursors. Phages which are able to catalyze formation of the self-assembling reaction product (via amide condensation) acquire an aggregate of reaction product, enabling separation by centrifugation. The thus selected phages can be amplified by infection of Escherichia coli. These phages are shown to catalyze amide condensation and hydrolysis. Kinetic analysis shows a minor role for substrate binding. The approach enables discovery and mass-production of biocatalytic phages.

No / We demonstrate the self-assembly of bola-amphiphile-type conjugates of dipeptides and perylene bisimide (PBI) in water and other polar solvents. Depending on the nature of the peptide used (glycine-tyrosine, GY, or glycine-aspartic acid, GD), the balance between H-bonding and aromatic stacking can be tailored. In aqueous buffer, PBI-[GY]2 forms chiral nanofibers, resulting in the formation of a hydrogel, while for PBI-[GD]2 achiral spherical aggregates are formed, demonstrating that the peptide sequence has a profound effect on the structure formed. In water and a range of other polar solvents, self-assembly of these two PBI-peptides conjugates results in different nanostructures with highly tunable fluorescence performance depending on the peptide sequence employed, e.g., fluorescent emission and quantum yield. Organogels are formed for the PBI-[GD]2 derivative in DMF and DMSO while PBI-[GY]2 gels in DMF. To the best of our knowledge, this is the first successful strategy for using short peptides, specifically, their sequence/structure relationships, to manipulate the PBI nanostructure and consequent optical properties. The combination of controlled self-assembly, varied optical properties, and formation of aqueous and organic gel-phase materials may facilitate the design of devices for various applications related to light harvesting and sensing.

Yes / Phenylacetyl-peptide amphiphiles were designed, which upon cleavage by a disease-associated enzyme reconfigure from micellar aggregates to fibres. Upon this morphological change, a doxorubicin payload could be retained in the fibres formed, which makes them valuable carriers for localised formation of nanofibre depots for slow release of hydrophobic anticancer drugs.

Miniaturization of electronic circuits and systems continue to pose great difficulties in meeting the demand and anticipated growth for information services and their associated electronics. Of the several information processing techniques under consideration for devices of the future, optical systems are considered to offer significant advantages in terms of speed and bandwidth. Unfortunately, at the dimensions of contemporary electronics, optical waveguides will fail to assist significantly due to the fact that standard optical waveguides will have dimensions below the diffraction limit and hence optical waveguiding at such scales will be impractical. In order to circumvent this, recent work in the area of using nano-sized protrusions to guide light below the diffraction limit has been receiving a decent amount of attention. Such systems have typically involved using electron beam lithography to create these perturbations on metallic surfaces called plasmonic waveguides. While these waveguides are fairly efficient, in the amounts required to make real circuits this method would be impractically slow and prohibitively expensive. However, such waveguides could be made much more cheaply if means could be found to arrange colloidal nanoparticles on suitable substrates. In this project, nanoscale self-assembly has been investigated with the aim of achieving such ends. Colloidal nanoparticles have been synthesized and self-assembled onto substrates such that they show near field interactions necessary for plasmonic waveguiding without any aggregation. Absorption peak shifts, which were obtained during the experimental phase of this project confirmed that such nanoparticle assemblies can be achieved and that they do demonstrate some plasmonic waveguiding action. With this first step, it is hoped that films like these may find use for quick and cheap plasmonic waveguiding sometime in the near future. / Master of Science

Structures in nature exhibit unique and complex architectures whose order propagates from nano- (10-9 m) to macro-scales (mm to m). These structures give rise to a rich diversity of adaptive function that allows for life in all environments on Earth. This complex functionality has driven research into bio-inspired materials where scientists investigate the complex relationship between sequence, structure and function of these materials. A good illustrative example of the effect that hierarchical structure can have is a brick wall. Bricks are laid so that the layer on top is shifted in either direction by half of a brick. This alternating pattern is what gives the wall its strength. If a crack occurs in the mortar, it will only propagate until it hits a boundary (a neighboring brick). Designing nanostructures can have similar effects on materials we use every day. Some of the most prevalent are adhesives that mimic the structures on gecko feet, which allow them to stick to any surface. This work presents bottom-up design strategies for self-assembling protein materials whose hierarchical structure may prove useful in a variety of applications in soft-robotics and energy storage. Proteins are a useful class of molecules, because they contain a level of structural complexity beyond that of synthetic materials. They are an inherently 'green' material feedstock; made in a lab using microbes like E. coli. Additionally, with the ease and availability of genetic engineering techniques we can easily modify the structure. This is especially true for the class of proteins, repeat proteins, which are the focus of this manuscript. Repeat proteins comprise small repeated sequences which are structurally independent from each other and can be strung together to create open, extended architectures. Here we explore the self-assembly emergent properties of the consensus tetratricopeptide repeat (CTPR18) . We show that this protein assembles into highly ordered 1D and 2D arrays that are shape tunable based the molecular environment (solvents, charge, etc). These nanomaterials may prove useful as molecular recognition scaffolds. We further explore the hierarchical self-assembled films of CTPR18. These films form highly oriented lamellar structures that seemingly propagate the entire length of the films. These lamellae directly affect the materials mechanical properties. Accordingly, by changing the film casting conditions, we can impart a structural gradient in the film, which proves useful in tuning the water-induced bending motion of these films. Herein, we show the ability to change the speed and directionality of actuation by simply changing the underlying film morphology. Lastly, we show that these films are electroresponsive as well, owing this function to ion transport through the inherently charged character of CTPR18. These dual responsive materials may prove useful in soft robotics. Additionally we are beginning investigations into the usefulness of CTPR18 films as alternate materials for ion-transport materials like those used in lithium polymer (more commonly LiPo) and sodium-ion batteries. / PHD / Structures in nature exhibit unique and complex architectures whose order propagates from nano- (10⁻⁹ m) to macro-scales (mm to m). These structures give rise to a rich diversity of adaptive function that allows for life in all environments on Earth. This complex functionality has driven research into bio-inspired materials where scientists investigate the complex relationship between sequence, structure and function of these materials. A good illustrative example of the effect that hierarchical structure can have is a brick wall. Bricks are laid so that the layer on top is shifted in either direction by half of a brick. This alternating pattern is what gives the wall its strength. If a crack occurs in the mortar, it will only propagate until it hits a boundary (a neigh-boring brick). Designing nanostructures can have similar effects on materials we use every day. Some of the most prevalent are adhesives that mimic the structures on gecko feet, which allow them to stick to any surface. This work presents bottom-up design strategies for self-assembling protein materials whose hierarchical structure may prove useful in a variety of applications in soft-robotics and energy storage. Proteins are a useful class of molecules, because they contain a level of structural complexity beyond that of synthetic materials. They are an inherently ‘green’ material feedstock; made in a lab using microbes like E. coli. Additionally, with the ease and availability of genetic engineering techniques we can easily modify the structure. This is especially true for the class of proteins, repeat proteins, which are the focus of this manuscript. Repeat proteins comprise small repeated sequences which are structurally independent from each other and can be strung togeth-er to create open, extended architectures. Here we explore the self-assembly emergent properties of the consensus tetratricopeptide repeat (CTPR18) . We show that this protein assembles into highly ordered 1D and 2D arrays that are shape tunable based the molecular environment (sol-vents, charge, etc). These nanomaterials may prove useful as molecular recognition scaffolds. We further explore the hierarchical self-assembled films of CTPR18. These films form highly oriented lamellar structures that seemingly propagate the entire length of the films. These lamellae directly affect the materials mechanical properties. Accordingly, by changing the film casting conditions, we can impart a structural gradient in the film, which proves useful in tuning the water-induced bending motion of these films. Herein, we show the ability to change the speed and directionality of actuation by simply changing the underlying film morphology. Lastly, we show that these films are electroresponsive as well, owing this function to ion transport through the inherently charged character of CTPR18. These dual responsive materials may prove useful in soft robotics. Additionally we are beginning investigations into the usefulness of CTPR18 films as alternate materials for ion-transport materials like those used in lithium polymer (more com-monly LiPo) and sodium-ion batteries.

Flexible manufacturing is something that most companies is aiming to accomplish due to the increased demand for variety and a competitive global market. This thesis report includes an introduction to the automation concept and the development towards flexible automation. A general flexible assembly cell is presented and its content and requirements are discussed. The work has been done with focus on an assembly process with dedicated fixtures at VCE (Volvo Construction Equipment). Based on the literature review and the general example, a list of actions to take while planning and implementing a process is developed. The actions roughly include: mapping of the process, defining goals, investigation of automation level, holistic view while planning, definition of the need for flexibility, investment plan, designing and comparing concepts, investigation of possible issues and implementation in small scale. The current manual process at VCE is presented and analysed. Three concepts are designed with product flexibility as an alternative to processes in which traditional dedicated fixtures are used. The designed concepts are a fully automated concept, a hybrid concept with separated workspace and a human-robot collaboration. Finally, the concepts are analysed and compared based on following parameters: productivity, product cost, investment, flexibility, space requirement and setup time. One final comparing summary of the concepts is done. The analysis shows that a fully automated concept is to prefer in this case. However, a human-robot collaboration could be appropriate to use if the process is expected to improve with the human workforce. Examples of when it could be reasonable to use human-robot collaboration despite this are: if the task provides better quality when conducted by human or if the task is complex to automate.