<p>Large-scale, in vitro vaccine screening is an expensive and slow process, while rational vaccine design is faster and cheaper. As opposed to the emperical ways to design vaccines in biology laboratories, rational vaccine design models the structure of vaccines with computational approaches. Building an effective predictive computer model requires extensive knowledge of the process or phenomenon being modelled. Given current knowledge about the steps involved in immune system responses, computer models are currently focused on one or two of the most important and best known steps; for example: presentation of antigens by major histo-compatibility complex (MHC) molecules. In this step, the MHC molecule selectively binds to some peptides derived from antigens and then presents them to the T-cell. One current focus in rational vaccine design is prediction of peptides that can be bound by MHC.<p>Theoretically, predicting which peptides bind to a particular MHC molecule involves discovering patterns in known MHC-binding peptides and then searching for peptides which conform to these patterns in some new antigenic protein sequences. According to some previous work, Hidden Markov models (HMMs), a machine learning technique, is one of the most effective approaches for this task. Unfortunately, for computer models like HMMs, the number of the parameters to be determined is larger than the number which can be estimated from available training data.<p>Thus, heuristic approaches have to be developed to determine the parameters. In this research, two heuristic approaches are proposed. The rst initializes the HMM transition and emission probability matrices by assigning biological meanings to the states. The second approach tailors the structure of a fully connected HMM (fcHMM) to increase specicity. The effectiveness of these two approaches is tested on two human leukocyte antigens(HLA) alleles, HLA-A*0201 and HLAB* 3501. The results indicate that these approaches can improve predictive accuracy. Further, the HMM implementation incorporating the above heuristics can outperform a popular prole HMM (pHMM) program, HMMER, in terms of predictive accuracy.

In this thesis, we first present a variance estimation technique based on the standardized time series methodology for steady-state simulations. The proposed variance estimator has competitive bias and variance compared to the existing estimators in the literature. We also present the technique of rebatching to further reduce the bias and variance of our variance estimator. Second, we present two fully sequential indifference-zone procedures to select the best system from a number of competing simulated systems when best is defined by the maximum or minimum expected performance. These two procedures have parabola shaped continuation regions rather than the triangular continuation regions employed in several papers. The rocedures we present accommodate unequal and unknown ariances across systems and the use of common random numbers. However, we assume that basic observations are independent and identically normally distributed. Finally, we present procedures for finding a set of feasible or near-feasible systems among a finite number of simulated systems in the presence of multiple stochastic constraints, especially when the number of systems or constraints is large.

This study is to develop a 2D fully nonlinear numerical wave tank used to investigate the wave-induced dynamic properties of a dual pontoon floating structure (DPFS) with a liquid container on the top. The nonlinear numerical wave tank, developed based on the velocity potential function and the boundary element method (BEM), is to simulate dynamic properties including sway, heave, roll, and tension response. In addition, a physical model of the dual floating pontoon is tested in a hydrodynamic wave tank to validate the numerical model for simulation of wave and structure interaction. In the numerical model, a boundary integral equation method (BIEM) with linear element scheme is applied to establish a 2D fully nonlinear numerical wave tank (NWT). The nonlinear free surface condition is treated by combining the Mixed Eulerian and Lagrangian method (MEL), the fourth-order Runge-Kutta method (RK4) and a cubic spline scheme. The second-order Stokes wave theory is used to generate the velocity flux on the input boundary. Numerical damping zones are deployed at both ends of the NWT to dissipate or absorb the transmitted and reflected waves. Acceleration potential method and modal decomposition method are adopted to solve the unsteady potential functions £X1,t and £X2,t, while the system of motion equation is established according to Newton's 2nd law. Finally, the RK4 is applied to predict the motion of the platform, and the variation of free surface. As for the hydrodynamic laboratory model test, an image process scheme is applied to trace the floating structure motion and the variation of water surface inside the sloshing tank, while the mooring tension is measured by a load cell and stored in a data logger. The comparisons of numerical simulations and experimental data indicate that the numerical predictions are larger than measurements especially near the resonance frequency. This discrepancy is probably due to the fluid viscous effect. To overcome this problem and maintain the calculation efficiency, an uncoupled damping coefficient obtained through a damping ratio (£a=C/Ccr=0.02) is incorporated into the vibration system. Results reveal that responses of body motion near the resonant frequencies of each mode have significantly reduced and close to the measurements. Therefore, the suitable value of the damping ratio for the floating platform is £a=0.02. Then the numerical model with a damping ratio is applied to investigate the dynamic properties of the floating platform for different arrangements, including different mooring angle, spring constant, spacing, and the liquid container. Results demonstrate that the resonant frequency of each mode, responses of body motion and mooring tensions change along with the settings. As a whole, the platform with smaller mooring angle, longer spacing between the pontoons, higher water depth and wider width of the liquid container has relatively stable body motions and less mooring tension. Finally, the comparisons of the effects of random and regular waves on the floating structure illustrate that the variation of water surface in the liquid container is much severe in random waves than in regular waves such that the interaction between liquid and floating structure is more chaotic and thus reduces the amplitude of each response mode. As a result, the mooring tensions for random waves become much gentler than the regular waves. Key words: Boundary integral equation method; fully nonlinear numerical wave tank; dual pontoon floating structure

Polymer light emitting diodes (PLED) were using a heterocyclic aromatic rigid-rod polymer poly-p-phenylene-benzobisoxazole (PBO) as an opto-electronically active layer; and poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonic acid) (PEDOT:PSS) as a hole transporting layer. Aluminum (Al) and indium tin oxide (ITO) were served as device cathode and anode, respectively. [6,6]-phenyl C61-butyric acid methyl ester (PC61BM) or derivatized multi-wall carbon nano-tube (MWCNT-C18), with great electron transporting ability, was doped into PBO to enhance the performance of PLED devices as well as the thin-film electrical conductivity. The optical length was changed by using different spin coating speeds and durations. From the research, the £fmax of electroluminescence (EL) was blue-shifted as PEDOT:PSS spin coating speed increased for a thinner layer. Once using a higher spin coating speed repeatedly to coat PEDOT:PSS, the £fmax of electroluminescence was red-shifted. If the PEDOT:PSS film thicknesses were similar, the EL spectra were almost the same, independent of device processing scheme. The injection current and EL intensity were enhanced by doping PC61BM or MWCNT- C18. The electric conductivity parallel to film surface (£m¡ü) was increased as the doping concentration increased. Because of the extremely different aspect ratio, the MWCNT-C18 had a lower percolation threshold concentration. Therefore, at a low MWCNT-C18 doping concentration, the injection current and the EL intensity were enhanced compared with those of PC61BM.

The main purpose of this thesis is to explore whether the Balassa-Samuelson hypothesis can effectively explain the long-term change of the real exchange. The recent panel unit root, panel cointegration tests and fully modified OLS are applied to examine the four tested equations that are based on the Balassa-Samuelson hypothesis. 1. Relative differential productivity between traded and non-traded sectors influences price differential in two sectors. 2. We extend the relative productivity in non-traded and traded sectors causing change in non-traded relative price into the two-country model. 3. The appreciation (depreciation) of the real exchange results from the different relative price of the two-country model. 4. The appreciation (depreciation) of the real exchange is caused by the different relative productivity of the two-country model. The data span is from 1971 to 1995, and includes 12 OECD countries. There are three main different points from the existing literatures. 1. We apply some newly developed panel unit root tests to estimate the equations based on Balassa-Samuelson hypothesis. 2. The previous documents only estimated the model of one variable, but the estimation of two variables was rare. In the equation 14 and 15, we examined the two variables in both. 3. In the calculation of the price, owing to the difficulties of collecting data from various sectors, we use a special way to measure the price. Finally, we can observe from the results of the empirical study: when productivity of the domestic sectors differentiates, that is, 1% increase in relative productivity between traded and non-trade sectors causes 0.53% increase in domestic relative prices. When it is taken into the two-country model, the increase of productivity will cause the appreciation of the real exchange rate. This can explain why in the developed countries like the U.S. and Japan, the faster increase in domestic relative productivity causes the appreciation of real exchange rates in the long run.

Opto-electronics of non-fully conjugated molecules was demonstrated successfully in this research as light emitting diodes (LEDs). A series of benzoxazole poly[2,2-(m-2-hydroxyl phenylene)-4-4¡¦-hexafluoroisopro- pane-bibenzoxazoles] (6F-PBO-OH, Am) and benzimidazole poly[2,2¡¦- (2-hydroxy-o-phenylene)-5,5¡¦-bibenzimiazole] (OH-Pbi, B(1-m)) were copolymerized for coil-like non-fully conjugated poly-(Am-co-B(1-m)) for luminescence investigation. UV-Vis absorption of the non-fully conjugated copolymers showed superposition of individual absorption response from the two chemical components of the copolymer. However, the photoluminescence (PL) and the electroluminescence (EL) emissions had a red shift with increasing OH-Pbi content. It seemed to suggest that OH-Pbi was more charge delocalized than 6F-PBO-OH. In mono-layer LEDs, the diode threshold voltages were about at 2 ~ 3 V and the EL showed a green emission. Tunable emission was not observed in varying the m value of the copolymers. Composites of copolymer, poly(Am-co-B(1-m)) and multi-wall carbon nanotube (MWNT) were in-situ synthesized for mono-layer LED fabrication. Few MWNT aggregation was observed via the field-emission scanning electron microscopy. It was a success in dispersing MWNT in the copolymers. There was a red shift with MWNT addition in the PL and the EL emissions. The diode threshold voltages were about at 2 ~ 5 V and the EL emission still showed a green emission. According to this study, MWNT was inconsequential on the PL and the EL emissions of the copolymers up to 2 wt. %.

The main purpose of this thesis is to explore whether the Balassa-Samuelson hypothesis can effectively explain the long-term change of the real exchange. The recent panel unit root, panel cointegration tests and fully modified OLS are applied to examine the four tested equations that are based on the Balassa-Samuelson hypothesis. The data span is from 1985 to 2002, and includes 7 east asian countries. 1. Relative differential productivity between traded and non-traded sectors influences price differential in two sectors. 2. We extend the relative productivity in non-traded and traded sectors causing change in non-traded relative price into the two-country model. 3. The appreciation (depreciation) of the real exchange results from the different relative price of the two-country model. 4. The appreciation (depreciation) of the real exchange is caused by the different relative productivity of the two-country model. Finally, we can observe from the results of the empirical study: when productivity of the domestic sectors differentiates, that is, 1% increase in relative productivity between traded and non-trade sectors causes 0.28% increase in domestic relative prices. When it is taken into the two-country model, the increase of productivity will cause the appreciation of the real exchange rate.

Polymer photovoltaic cell (PV cell) utilizes a polymer to absorb photons for generating excitons. When excitons are separated into electrons and holes, the device has the photovoltaic effect. Polymer light emitting diode (PLED) injects electrons and holes respectively from cathode and anode into a polymer emission layer. Some of the electrons and the holes would recombine to induce light emission. This research used a heterocyclic aromatic rigid-rod polymer poly-p-phenylene- benzobisoxazole (PBO) as the opto-electronic layer, and a conducting material of poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonic acid) (PEDOT:PSS) as the hole transport layer. PV cells were fabricated using indium-tin-oxide (ITO) as anode and aluminium as cathode. Same layer arrangement was applied for PLEDs. These two kinds of devices were measured for electrical and optical response. It was evidenced that the addition of PEDOT:PSS layer facilitated the separation of excitons into electrons and holes at the PBO/PEDOT:PSS interface. Insertion of a LiF layer between PBO layer and Al cathode reduced their energy band gap and facilitated charge transport leading to an enhanced efficiency for PV cells and PLEDs. Thickness variations were found on spun PBO layer. According to emission intensity, we knew that the PBO layer quality was significant for electroluminescence. Introduction of a PEDOT:PSS layer improved the interface between ITO and PBO. The thickness of PEDOT:PSS layer depended on the ITO surface roughness. With a PEDOT:PSS layer, the opto-electronic efficiency of PV cell and PLED was improved.

Luminescent emission of non-fully conjugated homopolymers was successfully demonstrated as light emitting diodes (LEDs) in this research. Coil-like heterocyclic aromatic poly[2,2-(2,5-dialkyloxyphenylene)-4-4¡¦-hexafluoroisopropanebibenzoxazo- les] (6F-PBO-CnOTpA, with n = 10, 15, and 20) was synthesized, and polymer composites of 6F-PBO-CnOTpA was in-situ synthesized with acidified multi-wall carbon nanotube (MWNT- COOH). The non-fully conjugated coil-like heterocyclic aromatic homopolymer was synthesized by reacting 2,2,bis-(3-amino-4-hydroxy[henyl]-hexafluoropropane with 2,5-dialkyloxyterephthalic acid (CnOTpA) for 6F-PBO-CnOTpA, with n = 10, 15, and 20. In addition, MWNT was acidified for connecting the carboxylic group (-COOH) to reduce its aspect ratio and entropy induced aggregation. MWNT-COOH was analyzed using elemental analysis (EA) and viscometry to validate the effects of acidification period. The EA result seemed to suggest that the oxygen content increased, and the carbon and the hydrogen contents decreased with acidification period. The inherent viscosity (£binh) decreased according to acidification period suggesting that the aspect ratio was indeed decreased. A hole transport layer of PEDOT¡GPSS was applied for multi-layer LEDs,. The LEDs all showed a threshold voltage about 4 V also for the composites of 6F-PBO-CnOTpA in-situ polymerized with MWNT-COOH. The 6F-PBO-CnOTpA LEDs with and without MWNT-COOH showed an electroluminescence emission range of 400 to 750 nm.

A 2D fully nonlinear Numerical Wave Tank (NWT) is developed based on the potential theory, mixed Eulerian-Lagrangian (MEL) time marching scheme, and boundary element method (BEM). Nonlinear Wave deformation and wave forces on stationary and freely floating bodies are calculated using the NWT. For verification, the computed mean, 1st, 2nd, and 3rd order wave forces on a single submerged cylinder are compared with those of Chaplin's experiment, Ogilvie's 2nd-order theory, and other nonlinear computation called high-order spectral method. Similar calculations for dual submerged cylinders are also conducted. The developed fully nonlinear NWT is also applied to the calculations of the nonlinear pressure and force of surface piercing barge type structures and these obtained results agree with experimental and theoretical results. Nonlinear waves generated by prescribed body motions, such as wedge type wave maker or land sliding in the coastal slope area, can also be simulated by the developed NWT. The generated waves are in agreement with published experimental and numerical results. Added mass and damping coefficients can also be calculated from the simulation in time domain. For the simulation of freely floating barge-type structure, only fully nonlinear time-stepping scheme can accurately produce nonlinear body motions with large floating body simulations. The acceleration potential method, which was developed by Tanizawa (1996), is known to be the most accurate, consistent and stable. Using acceleration potential method, in the present study, the series of motions and drift forces were calculated over a wide range of incident wave frequencies including resonance region. To guarantitatively compare the nonlinear contribution of free-surface and body-boundary conditions, the body-nonlinear-only case with linearized free-surface condition is separately simulated. All the floating body motions and forces are in agreement with experimental results. Finally, the NWT is extended to fully nonlinear wave-body-current interactions of freely floating bodies, which has not been published in the open literature until now.