Glycerol monooleate (GMO) is a common engine oil lubricant additive used to reduce friction and wear in engines. The aim of this thesis is to investigate the properties of GMO in bulk and under confined conditions with shear using molecular dynamics simulations. The self-assembly of GMO into reverse micelles (RMs) in toluene and n-heptane solvents is studied at a range of concentrations and subsequently with several common engine impurities over simulation timescales of 5-30 ns. The dimensional properties of the RMs are found to correspond well with experimentally studied SANS/SAXS measurements. Secondly, the properties of GMO confined between mica surfaces are studied under quiescent and shear conditions. Under shear, the performance of GMO as a friction modifier is studied and the structural and frictional properties are examined. In particular, the mass density and velocity profiles of the fluid are used to gain insights into the structure and dynamics of the confined GMO fluid films, under a variety of shear rates and surface separation. The data is found to fit excellently to the universal friction curve. Following this the effect of hydrolysing the GMO to oleic acid is studied in bulk and under shear, it is found that increasing oleic acid concentration typically reduces the propensity to self-assemble and under confinement increases the friction coefficient. And finally, a study on a range of other similar surfactants is conducted to investigate the effect of unsaturation, head group and chain length on the calculated friction coefficient and the structure of the surfactant films.

The question about the origins of life often appears as a difficult question to answer. A more reliable candidate molecule for the chemical origins of life would be a molecule that is capable of making copies of itself from simple precursors. With the finding of the catalytic activities of RNA molecules by Thomas Cech and Sid Altman in late 1980s, the term ribozyme was introduced to define an RNA molecule with catalytic activity. The RNA World is a conceptual period in the early stages in the development of life because RNA simultaneously possesses evolvability and catalytic function. An RNA molecule that could evolve in such a fashion is likely to have been one of the Earth's first life forms. The most important problem facing the RNA World is the difficulty of prebiotic synthesis of RNA. Different prebiotic environments could provide the right reaction conditions for synthesis of catalytically active RNA molecules. Most importantly, these environments can support new ways to assemble monomers into polymers. In order to understand and demonstrate how small inactive RNA oligomers can self-assemble into an autocatalytic ribozyme molecule, here I have used the Azoarcus Group I intron. First, the fragmentation and the self-assembly reactions were done using the natural IGS-tag combination of the Azoarcus group I intron, which is GUG/CAU. The main purpose was to experimentally demonstrate that the ribozyme can be broken down into five or more shorter RNA fragments and these fragments can self-assemble into a catalytically active covalent full-length molecule. Then, with the successful demonstration that five inactive RNA fragments can self-assemble, the next step to test the other possible breaking locations with mutated IGS/tag combinations. A new IGS/tag pair GCG-CGU also successfully demonstrated the five-piece self-assembly reaction. Finally, we tested these reactions in different Mg2+ concentrations to optimize the self-assembly reactions. By focusing not only one single reaction but on a collection of different sequence requirement combinations and with the development of evaporation and subsequent rehydration by spinning down methods this study successfully illustrates that covalent self-assembly from inactive RNA oligomers is possible. Therefore, this thesis work focuses on a more broader aspect of intermolecular interactions in the study of the RNA World, as illustrated in following chapters.

Doctor of Philosophy (PhD) / Oligomeric surfactants, sometimes referred to as gemini surfactants, consist of two or more amphiphilic ‘monomer’ units linked together by spacer groups. The chemical identity of the spacer group is unconstrained, and it joins the individual units at or near the hydrophilic headgroups. Oligomeric surfactants display a range of interesting properties, including very low critical micelle concentrations, high surface activity and unusual rheology and self-assembly. Consequently they have many potential applications, both scientific and industrial. Until now, their use has been limited by the cost of their synthesis, which in some cases involve long and difficult procedures. This project developed from the idea that a synthesis based on polymerization could prove a useful and versatile method for producing these surfactants. The chemical starting point for this project was a series of polymerizable surfactants (‘surfmers’), upon which polymerization was performed. Two families of surfmers were investigated, both cationic and based on methacrylate and vinylpyridinium moieties respectively. The physical behaviour of these surfactants – a number of which are new – was investigated using standard techniques; these included the determination of the critical micelle concentration, characterization of phase behaviour, neutron scattering and surface adsorption. In producing oligomers, the initial focus was on free-radical polymerization, with control of molecular weight to be achieved by chain-transfer techniques. Due largely to analysis problems, this work proved unsuccessful. In its place a new reaction, not based on conventional polymerization methods, has been developed. The vinylpyridinium surfmers mentioned above readily undergo addition across the double bond to produce alkyl ring substituents. Under basic conditions, these alkylpyridiniums undergo an elimination/addition reaction in which they link together to form oligomers. This reaction can be started or stopped by raising or lowering the pH of the reaction solution, and has been performed in both organic and aqueous solutions. It is referred to in this thesis as LELA(Linkage by ELimination/Addition). The LELA reaction was used to produce mixtures of oligomers, the phase behaviour and surface adsorption of which were examined. Small-angle neutron scattering was used to monitor the reaction in real time and identify changes in self-assembly as the average oligomer length increased. Progress was also made towards a chromatographic protocol that would allow mixtures to be separated into their components and the pure oligomers to be studied. Finally, some of the compounds studied display interesting pH-dependent chromophoric properties which were also found to occur with other simple alkylpyridinium species. They are tentatively ascribed to inter- and intramolecular charge-transfer complexes, and evidence towards this conclusion was collected and is presented along with relevant calculations.

Gold (Au) implantation in silicon (Si) has been a topic of great interest from both fundamental and applied perspectives. Ion implantation is a versatile technique due to its ability to form surface-embedded nanoparticles that provide better adhesion. Also, being an integral part of the substrate lattice, the nanoclusters produced by ion implantation are free from impurities and their size distribution can be controlled by carefully optimizing the beam parameters. During our experiments to produce nanoclusters of Au on Si for use as seeds for the growth of nanowires, we stumbled across an unusual pattern formation process under specific conditions. This unique self-assembly process is observed only within a critical threshold implantation fluence and above a threshold annealing temperature. Fabrication of ordered arrays of metal nanoparticles on Si substrates is of significance for both fundamental science associated with low-dimensional physics and technical app lications. The application of functional nanostructures strongly depends on their assembly in ordered one- or two- dimensional arrangements. These arrangements may play an important role in fabricating ordered arrays of semiconductor/oxide nanowires.This thesis discusses a systematic study performed to understand the temperature and time dependent nucleation, growth of Au nanoclusters and evolution of the self-assembled patterns. A growth model is proposed to show the re-crystallization behaviour of Au supersaturated amorphous silicon (a-Si) on Si substrate. The observed self-assembled periodic patterns of Au nanoclusters bear resemblance to the Liesegang ring structures prevalent in some chemical reaction-diffusion systems. Based on this systematic study of the growth and morphology of Au nanoclusters, a tentative growth mechanism has been proposed for the formation mechanism of this unusual self-assembled pattern. The pattern formation of this non-equilibrium process is expected to originate due to instabilities of the three scales of Au nanoclusters at elevated temperatures. The kinetics of pattern formation from a supersaturated solid solution (a-Si/Au alloy) is demonstrated using numerical solutions obtained by a two-dimensional growth model, which takes into account the nucleation, diffusion and the aggregation process. The numerical solution of the diffusion equations appear to be in good agreement with the experimental results.

The binding affinity of single stranded DNA (ssDNA) for gold nanoparticle surface is studied in this work. The data indicate that the strength of interaction between ssDNA and Au particle surface is closely related to the particle size, with smaller particles (5 nm) producing the most pronounced effects. From these experimental findings, a single stranded DNA (ssDNA) based method to assimilate 13 and 5 nm gold nanoparticles was developed, and verified by transmission electron microscopy (TEM). / Singapore-MIT Alliance (SMA)

Thesis (Ph.D.)--University of Delaware, 2006. / Principal faculty advisors: Dionisios G. Vlachos and Raul F. Lobo, Dept. of Chemical Engineering Includes bibliographical references.

Thesis (Ph.D.)--University of Delaware, 2006. / Principal faculty advisor: Mary E. Galvin-Donoghue, Dept. of Materials Science & Engineering. Includes bibliographical references.

This thesis describes the fabrication and characterization of integrated hollow Bragg waveguides fabricated by controlled thin film buckling. Hollow waveguides based on two different set of materials were studied. In the first case, thermal tuning of air-core dimensions was studied using waveguides, with chalcogenide glass and polymer claddings. Results showed that the change in air- core height as a function of small temperature variations was in good agreement with theory. Planar, silicon based, hollow core waveguides with Si/SiO2 Bragg reflector claddings are also described. Fabrication was accomplished by incorporating compressive stress in the sputtered Si and SiO2 layers and then heating samples to induce buckling along predefined areas of low adhesion. Several low adhesion layers were studied, but a fluorocarbon layer was deposited by CVD gave the best results. Optical experiments demonstrated optical confinement in the air-core, with loss in the ~5 dB/cm range at the 1550 nm wavelength. / Photonics and Plasmas

Thesis (Ph. D.)--University of Delaware, 2006. / Principal faculty advisor: Darrin J. Pochan, Dept. of Materials Science & Engineering. Includes bibliographical references.

A number of compounds were synthesized with the ultimate goal being the synthesis of C₂ symmetric molecules which displayed thermotropic liquid crystalline behaviour. The compounds prepared were 4-alkoxy benzophenones, 3,4-bis-alkoxy benzophenones, 4- alkoxy dibenzylidene acetones, 3,4-bis-alkoxy dibenzylidene acetones and 4-alkoxy- 1, 9-diphenyl-nona-l,3,6,8-tetraen-5-ones. The length of the linear alkoxy side chain was varied from C₆H₁₃ to C₁₂H₂₅. All compounds were characterized by FTIR, ¹H, and ¹³C NMR spectroscopy. Mesophase behaviour of the synthesized compounds was investigated using differential scanning calorimetry and polarizing optical microscopy. It was determined that both the alkoxy side chain length, as well as the number of alkoxy side chains have an effect on the ability of this class of C₂ symmetric compounds to selfassemble into liquid crystalline phases. In addition, the overall core size and extent of conjugation also affected mesophase formation. The mono-alkoxy benzophenones and dibenzylidene acetones were non-mesogenic, while all four of the mono-alkoxy 1,9- diphenyl-nona-l,3,6,8-tetraen-5-ones (alkoxy side chain of lengths C₆H₁₃, C₈H₁₇, C₁₀H₂₁ and C₁₂H₂₅)self-assembled into nematic liquid crystalline phases. Increasing the number of alkoxy side chains from one to two per aromatic moiety helped induce liquid crystalline formation: the corresponding bis-C₆H₁₃ benzophenone and bis-C ₆H₁₃, bis C₈H₁₇, and bis-C₁₀H₂₁ dibenzylidene acetones were mesogenic, displaying smectic A (benzophenone) and nematic (dibenzylidene acetone) mesophases respectively.