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.

The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.

The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.

Seeding is an important variable in controlling or directing the assembly of peptides. The presence of impurities, responsible for creating a 'dip' in the surface tension versus peptide concentration profile, is used to determine the critical aggregation concentration (CAC). This phenomenon is investigated to differentiate crude and high purity EAK16-II peptide. The purified peptide did not show this 'dip' and clearly indicated a critical aggregation concentration for EAK16-II at 0. 09 mg/mL by surface tension measurements. Conversely, a surface tension 'dip' is clearly observed for the crude EAK16-II peptide. Atomic Force Microscopy imaged the nanostructures of aggregates. The presence of impurities induces fibre formation below the CAC. This study provides information about the seeding effect of peptide assembly at low concentrations as well as the modification of surface activity of assembled peptide particles. Alanine, glutamic acid and lysine were used as model seeding agents to simulate the seeding phenomenon and better understand the nucleation mechanism of peptide assembly. All amino acid monomers were able to induce fibre formations at low peptide concentrations. However, only glutamic acid and lysine were able to produce the surface tension dip profile observed in the crude peptide. This information may be of importance in understanding fibrillogenesis occurring in conformational diseases and other biomedical applications including drug delivery.

ABSTRAKT Det här är en sammanfattning av den formella delen av vårt projektarbete. Under hösten 2007 och våren 2008 har vi på uppdrag av Egon Nilsson överhalat en hjälpmaskin ombord på Calmare Nyckel. Maskinen var i stort behov av en renovering, det läckte både kylvatten och smörjolja på olika ställen. Det har varit mycket väntetid på reservdelar eftersom maskinen är ovanlig och tillverkas i England. Mot slutet av arbetet råkade vi på bekymmer med vattenläckage i smörjoljan som gjorde att jobbet blev försenat några veckor. Läckaget lagades och maskinen provkördes. Resultatet blev bra, maskinen fungerade och gick som den skulle. Under arbetets gång har vi försökt i möjligaste mån följa de instruktioner som finns i instruktionsboken. När man genomför ett projektarbete av den här typen, skall all dokumentation rörande projektet redovisas. Materialet som presenteras i den här sammanställningen är upplagt enligt följande. Inledning till ämnet och projektet vilket följs av avsnitten projektprocessen och resultat. Till denna dokumentation har vi bifogat, arbetsdagbok och offert. / ABSTRACT This is a summary of the formal part of our project. During the autumn of 2007 and spring 2008 we have done an overhaul on one of the auxiliary engines onboard Calmare Nyckel. The assignment was given from Egon Nilson. The engine was in bad shape, lubrication oil and coolingwater was leaking from several cylinders and thereby in big need of a service. There have been some waiting time during the order of new parts because of the rare engine type which are British and therefore all the parts had to be ordered from England. At the end of the project we discovered some difficulties with coolingwater leaking in to the oil sump, this causing further delays finishing the project. The problem were solved and at the test run the engine run satisfactory. During the project we have as far as possible followed the manual and other instructions available. During a project like this it is important that all documentation of the project is shown. The materials that are shown are presented with an introduction followed by the process and the result. To this documentation we have attached a working diary and quotations.

Seeding is an important variable in controlling or directing the assembly of peptides. The presence of impurities, responsible for creating a 'dip' in the surface tension versus peptide concentration profile, is used to determine the critical aggregation concentration (CAC). This phenomenon is investigated to differentiate crude and high purity EAK16-II peptide. The purified peptide did not show this 'dip' and clearly indicated a critical aggregation concentration for EAK16-II at 0. 09 mg/mL by surface tension measurements. Conversely, a surface tension 'dip' is clearly observed for the crude EAK16-II peptide. Atomic Force Microscopy imaged the nanostructures of aggregates. The presence of impurities induces fibre formation below the CAC. This study provides information about the seeding effect of peptide assembly at low concentrations as well as the modification of surface activity of assembled peptide particles. Alanine, glutamic acid and lysine were used as model seeding agents to simulate the seeding phenomenon and better understand the nucleation mechanism of peptide assembly. All amino acid monomers were able to induce fibre formations at low peptide concentrations. However, only glutamic acid and lysine were able to produce the surface tension dip profile observed in the crude peptide. This information may be of importance in understanding fibrillogenesis occurring in conformational diseases and other biomedical applications including drug delivery.

In this study, we develop self-assembled nano-metal-dots etching mask techniques to fabricate quantum dots (QDs) nano-pillars. We explain the self-assembled nano-metal-dots formation processes by using Dewetting model. Two important experimental factors including (1) interaction force between film and vapor during annealing (£^FV),¡]2¡^interaction force between film and substrate (£^FS) are study to investigate the self-assembled processes. A 200nm thick SiO2 buffer layer is first deposited on the GaAs substrate to congregate thermal energy during the RTA process. In our group, the QDs optimum grown temperature condition is 570¢J, so we develop Au-Ge nano-dots process especially for GaAs based QDs samples. The 8nm thick Au-Ge is annealed at lower 500oC for 60sec under the pressure of 5 E6 Torr to format the nano-dots on QDs samples. The Au-Ge nano-dots have a size and density of 250 ¡Ó 50 nm and 4 E8 cm-2,respectively. We use the Au-Ge nano-dots as mask and dry etching process to fabricate the 9-layer vertical coupled QDs nano-pillars. The diameter and height of the QDs nano-pillar are 250, and 800nm, respectively. According to the QDs density, each nano-pillar contains 1600 QDs in it. The QDs nano-pillar resonance signals are observed by the low temperature cryogenic cathode-luminescence measurement. A strong nano-pillar resonance signal in 1050 nm matched to our simulation results is observed.

This dissertation, which consists of four parts, is to (i) present a mixed integer programming model for the strategic design of an assembly system in the international business environment established by the North American Free Trade Agreement (NAFTA) with the focus on modeling the material flow network with assembly operations, (ii) compare different decomposition schemes and acceleration techniques to devise an effective branch-and-price solution approach, (iii) introduce a generalization of Dantzig-Wolf Decomposition (DWD), and (iv) propose a combination of dual-ascent and primal drop heuristics. The model deals with a broad set of design issues (bill-of-materials restrictions, international financial considerations, and material flows through the entire supply chain) using effective modeling devices. The first part especially focuses on modeling material flows in such an assembly system. The second part is to study several schemes for applying DWD to the productionassembly- distribution system design problem (PADSDP). Each scheme exploits selected embedded structures. The research objective is to enhance the rate of DWD convergence in application to PADSDP through formulating a rationale for decomposition by analyzing potential schemes, adopting acceleration techniques, and assessing the impacts of schemes and techniques computationally. Test results provide insights that may be relevant to other applications of DWD. The third part proposes a generalization of column generation, reformulating the master problem with fewer variables at the expense of adding more constraints; the subproblem structure does not change. It shows both analytically and computationally that the reformulation promotes faster convergence to an optimal solution in application to a linear program and to the relaxation of an integer program at each node in the branchand- bound tree. Further, it shows that this reformulation subsumes and generalizes prior approaches that have been shown to improve the rate of convergence in special cases. The last part proposes two dual-ascent algorithms and uses each in combination with a primal drop heuristic to solve the uncapacitated PADSDP, which is formulated as a mixed integer program. Computational results indicate that one combined heuristic finds solutions within 0.15% of optimality in most cases and within reasonable time, an efficacy suiting it well for actual large-scale applications.

Electric field guided assembly of colloids is a new area of research in colloidal science where sub-micrometer particles, or colloids, are assembled using patterned electrodes. The design of these devices is often limited by an inability to characterize accurately forces and fluxes with linearized electrokinetic theory. The research presented in this dissertation describes an application of the finite element method to the nonlinear electrokinetic equations. The finite element model thus developed is then used to describe the nonlinear electrophoretic mobility of a dilute colloidal dispersion, investigate hydrodynamic and electric particle-particle interactions, and characterize particle-surface interactions. The effect of Stern layer conduction on the electrophoretic mobility and dielectric response is included using the generalized dynamic Stern layer model. The electrokinetic force is calculated using the Maxwell stress tensor method rather than the effective dipole method as it is more consistent with nonlinear electrokinetic theory. Significant results of this dissertation demonstrate the effect of nonlinear electrokinetic phenomena and extend the present electrokinetic theory. The calculation of nonlinear electrophoretic mobility of a dilute colloidal dispersion, which is valid for arbitrary particle surface charge or zeta potential, applied (AC) electric field strength, and applied AC electric field frequency. Also, the adsorption isotherm used by the generalized dynamic Stern layer theory is extended to include non-equilibrium reaction kinetics. This results in a model for Stern layer conduction which is valid for frequencies above 1 MHz. The utilization of the Maxwell stress tensor method results in a finite element model which is valid for arbitrary electric field strength and includes the effects of traveling-wave dielectrophoresis a nonlinear electrokinetic phenomena resulting from non-uniform electric field phase.

Development of nanoscience and nanotechnology requires rapid and robust nanomanufacturing processes to produce nanoscale materials, structures and devices. The dissertation aims to contribute to two major challenging and attractive topics in nanomanufacturing. Firstly, this research develops fabrication techniques for three dimensional (3D) structures and integrates them into functional devices and systems. Secondly, a novel process is proposed and studied for rapid and efficient manipulation of nanomaterials using a directed self-assembly process. The study begins with the development of nanoimprint lithography for nanopatterning and fabrication of 3D multilayer polymeric structures in the micro- and nano-scale, by optimizing the layer-transfer and transfer-bonding techniques. These techniques allow the integration of microfluidic and photonic systems in a single chip for achieving ultracompact lab-on-a-chip concept. To exemplify the integration capability, a monolithic fluorescence detection system is proposed and the approaches to design and fabricate the components, such as a tunable optical filter and optical antennas are addressed. The nanoimprint lithography can also be employed to prepare nanopatterned polymer structures as a template to guide the self-assembly process of nanomaterials, such as single-walled carbon nanotubes (SWNTs). By introducing the surface functionalization, electric field and ultrasonic agitation into the process, we develop a rapid and robust approach for effective placement and alignment of SWNTs. These nanomanufacturing processes are successfully developed and will provide a pathway to the full realization of the lab-on-a-chip concept and significantly contribute to the applications of nanomaterials.