I studied a family of closely connected topics related to the production and application of ultrashort laser pulses. I achieved broadband cascade Raman generation in crystals, producing mutually coherent frequency sidebands which can possibly be used to synthesize optical pulses as short as a fraction of a femtosecond (fs). Unlike generation using gases, there is no need for a cumbersome vacuum system when working with room temperature crystals. Our method, therefore, shows promise for a compact system. One problem for sideband generation in solids is phase matching, because the dispersion is significant. I solved this problem by using non-collinear geometry. I observed what to our knowledge is a record-large number of spectral sidebands generated in a popular Raman crystal PbWO4 covering infrared, visible, and ultraviolet spectral regions, when I applied two 50 fs laser pulses tuned close to the Raman resonance. Similar generation in diamond was also observed, which shows that the method is universal. When a third probe pulse is applied, a very interesting 2-D color array is generated in both crystals. As many as 40 anti-Stokes and 5 Stokes sidebands are generated when a pair of time-delayed linear chirped pulses are applied to the PbWO4 crystal. This shows that pulses with picosecond duration, which is on the order of the coherence decay time, is more effective for sidebands generation than Fourier transform limited fs pulses. I also studied the technique of fs coherent Raman anti-Stokes scattering (CARS) which is used as a tool for detecting dipicolinic acid, the marker molecule for bacterial spores. I observed that there is a maximum when the concentration dependence of the near-resonant CARS signal is measured. I presented a model to describe this behavior, and found an analytical solution that agrees with our experimental data. Theoretically, I explored a possible application for single-cycle pulses: laser induced nuclear fusion. I performed both classical and quantum mechanical calculations for a system of two nuclei moving under a superintense ultrashort field. From our calculation I noted that the nuclear collisions occur on a sub-attosecond time scale, and are predicted to result in an emission of zeptosecond bursts of light.

Phosphotriesterase (PTE) from Pseudomonas diminuta is a zinc metalloenzyme found in soil bacteria capable of organophosphate hydrolysis at rates approaching the diffusion controlled limit. Interest in PTE for degradation of chemical warfare agents and disposal of pesticides supports the need to understand the mechanism by which it performs hydrolysis. For further mechanistic clarity, this work will provide direct confirmation of the solvent bridge identity and the protonated species resulting in loss of catalytic identity. Inhibitor and product binding to the metal center will also be addressed; as well as the evaluation of the catalytic activity of Fe(II)-substituted PTE. This work has determined that the Mn/Mn-PTE electron paramagnetic resonance (EPR) spectrum exhibits exchange coupling that is facilitated through a hydroxide bridge. Protonation of the bridging hydroxide results in the loss of the exchange coupling between the two divalent cations and the loss of catalytic activity. The reversible protonation of the bridging hydroxide has an apparent pKa of 7.3 based upon changes in the EPR spectrum of Mn/Mn-PTE with alterations in pH. The pH-rate profile for the hydrolysis of paraoxon by Mn/Mn-PTE shows the requirement of a single function group that must be unprotonated with a pKa of 7.1. The comparable pKa values are proposed to result from the protonation of the same ionizable species. The effects of inhibitor and product binding on the magnetic properties of the metal center and the hydroxyl bridge are investigated by accessing new EPR spectral features. This work concludes that the binding of inhibitor occurs at the metal center and results in an increase of non-bridged hydroxyl species. These results, in conjunction with kinetic and crystallographic data, suggest that substrate binding via the phosphoryl oxygen at the ?-metal weakens the hydroxyl bridge coordination to the ?-metal. This loss of coordination would increase the nucleophilic character of the bridge, and binding of the substrate to the metal center would result in a stronger nucleophile for hydrolysis. Lastly, Fe(II) binding and activation of apoenzyme is evaluated under anaerobic conditions. This work concludes Fe/Fe-PTE is not catalytically active, but can bind up to 2 equivalent Fe(II) ions per active site.

Recent improvements in structural genomics efforts have greatly increased the number of hypothetical proteins in the Protein Data Bank. Several computational methodologies have been developed to determine the function of these proteins but none of these methods have been able to account successfully for the diversity in the sequence and structural conformations observed in proteins that have the same function. An additional complication is the flexibility in both the protein active site and the ligand. In this dissertation, novel approaches to deal with both the ligand flexibility and the diversity in stereochemistry have been proposed. The active site analysis problem is formalized as a classification problem in which, for a given test protein, the goal is to predict the class of ligand most likely to bind the active site based on its stereochemical nature and thereby define its function. Traditional methods that have adapted a similar methodology have struggled to account for the flexibility observed in large ligands. Therefore, I propose a novel fragment-based approach to dealing with larger ligands. The advantage of the fragment-based methodology is that considering the protein-ligand interactions in a piecewise manner does not affect the active site patterns, and it also provides for a way to account for the problems associated with flexible ligands. I also propose two feature-based methodologies to account for the diversity observed in sequences and structural conformations among proteins with the same function. The feature-based methodologies provide detailed descriptions of the active site stereochemistry and are capable of identifying stereochemical patterns within the active site despite the diversity. Finally, I propose a Markov Random Field approach to combine the individual ligand fragment classifications (based on the stereochemical descriptors) into a single multi-fragment ligand class. This probabilistic framework combines the information provided by stereochemical features with the information regarding geometric constraints between ligand fragments to make a final ligand class prediction. The feature-based fragment identification methodology had an accuracy of 84% across a diverse set of ligand fragments and the mrf analysis was able to succesfully combine the various ligand fragments (identified by feature-based analysis) into one final ligand based on statistical models of ligand fragment distances. This novel approach to protein active site analysis was additionally tested on 3 proteins with very low sequence and structural similarity to other proteins in the PDB (a challenge for traditional methods) and in each of these cases, this approach successfully identified the cognate ligand. This approach addresses the two main issues that affect the accuracy of current automated methodologies in protein function assignment.

Reusing code from software libraries can reduce the time and effort to construct software systems and also enable the development of larger systems. However, the benefits that come from the use of software libraries may not be realized due to limitations in the way that traditional software libraries are constructed. Libraries come equipped with application programming interfaces (API) that help enforce the correct use of the abstractions in those libraries. Writing new components and adapting existing ones to conform to library APIs may require substantial amounts of "glue" code that potentially affects software's efficiency, robustness, and ease-of-maintenance. If, as a result, the idea of reusing functionality from a software library is rejected, no benefits of reuse will be realized. This dissertation explores and develops techniques that support the construction of software libraries with abstraction layers that do not impede efficiency. In many situations, glue code can be expected to have very low (or zero) performance overhead. In particular, we describe advances in the design and development of active libraries - software libraries that take an active role in the compilation of the user's code. Common to the presented techniques is that they may "break" a library API (in a controlled manner) to adapt the functionality of the library for a particular use case. The concrete contributions of this dissertation are: a library API that supports iterator selection in the Standard Template Library, allowing generic algorithms to find the most suitable traversal through a container, allowing (in one case) a 30-fold improvement in performance; the development of techniques, idioms, and best practices for concepts and concept maps in C++, allowing the construction of algorithms for one domain entirely in terms of formalisms from a second domain; the construction of generic algorithms for algorithmic differentiation, implemented as an active library in Spad, language of the Open Axiom computer algebra system, allowing algorithmic differentiation to be applied to the appropriate mathematical object and not just concrete data-types; and the description of a static analysis framework to describe the generic programming notion of local specialization within Spad, allowing more sophisticated (value-based) control over algorithm selection and specialization in categories and domains. We will find that active libraries simultaneously increase the expressivity of the underlying language and the performance of software using those libraries.

In order to implement an accurate system that allows for absorption of reflected waves impinging to a wave maker (Active Reflection Absorption), it was required to apply a method to estimate properly the direction of arrival of the waves that does it in the fastest way possible. Our wavemaker control system has been prepared to handle an algorithm provided by Bosch-Rexroth where the wave angle estimation is practically locked to a very narrow frequency band (spatial gain-mixer). The system was evaluated with physical tests in a 3D wave basin for different conditions of reflected waves arriving with an angle to the wavemaker front, and acceptable performance has been found for the 3D ARA mode. However, for certain conditions over-compensation or sub-compensation can develop resulting in a poor absorption. This is mainly related to not being able to determine accurately the direction from which the reflected waves travel towards the wavemaker. The present work employed concepts found in the areas of antenna array signal processing and signal propagation, which were applied to this problem. This approach coupled naturally with our wavemaker system since it was prepared with 48 gages that can be employed in an array antenna fashion. A program was codified from an algorithm found in literature to calculate the Direction of Arrival (DOA) of the reflected waves. The focus for the testing of this program was with regular waves. The tests were conducted to validate the program with different angles of incidence and show that for regular waves the program was able to detect accurately the DOA of these in as few as 5 snapshots, with a minimum of 7 gages used as the antenna input. With data obtained directly from the control system of our wavemaker using regular waves, the program was able to determine the DOA. The computational burden of the algorithm is not significant in the case of regular waves. A modification of the program is required to analyze the DOA of reflected irregular waves, which could increase the computational burden. Actual implementation of this program to our control system depends on cooperation with Bosch-Rexroth.

Changes in the characteristics of the structure, such as damage, have not been considered in most of the active and semi-active control methods that have been used to control and optimize the response of civil engineering structures. In this dissertation, a direct adaptive control which can deal with the existence of measurement errors and changes in structural characteristics or load conditioning is used to control the performance of structures. A Simple Adaptive Control Method (SACM) is modified to control civil structures and improve their performance. The effectiveness of the SACM is verified by several numerical examples. The SACM is used to reduce the structural response such as drift and acceleration using active and semi-active devices, and its performance is compared with that of other control methods. Also, a probabilistic indirect adaptive control method is developed and its behavior is compared to the SACM using a simple numerical example. In addition to the simplicity of the SACM implementation, the results show that SACM is very effective to reduce the response of structures with linear and non-linear behavior in comparison with other control methods.

Low disturbance wind tunnels, such as the Klebanoff–Saric Wind Tunnel (KSWT), offer an ideal environment to study boundary layer transition. In particular, the leading-edge receptivity of sound can be measured by creating acoustic disturbances that interact with the leading edge of a model to create Tollmien–Schlichting Waves. The magnitude and composition (sound, turbulence) of the background disturbances can affect these experiments, so the background disturbances should be minimized and documented thoroughly. The purpose of this thesis is to document the background acoustic signature of the KSWT and describe infrastructure upgrades for acoustic receptivity experiments. The measurements presented in this thesis will support future receptivity measurements in the KSWT. Microphone measurements revealed several important acoustic features in the tunnel. Cross correlations showed that two sources of low-frequency unsteadiness (the extended diffuser and corner two) create large pressure fluctuations that dominate the pressure spectrum. Directional separation of waves in the test section revealed that motor and blade passing noise travels primarily upstream into the test section. Finally, the acoustic treatments in the plenum are effective at removing sound from the tunnel. A wall of speakers was installed in the plenum to enable acoustic receptivity experiments. The speakers create both the primary downstream traveling waves and reflected upstream traveling waves in the test section. An adaptive closed loop control system was installed to reduce the amplitude of the reflected waves during acoustic forcing. Although the performance of the control system is frequency dependent, the technique was implemented successfully. The reduction in the diffuser reflection will increase the quality of future acoustic receptivity experiments in the KSWT.

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The thesis aims to the research of active power factor correction (PFC) circuit and develop a DSP-based digital controller. In the thesis, PI controller is the control core for the voltage loop¡Band current loop, and then achieve the function of the power factor correction of boost converter. Finally, we develop a boost converter and connect it to a DSP-based controller to measure the waveforms and verify the power factor correction. Furthermore, the research can be extended to a simulating platform which we can verify the power factor correction by just changing the control law on DSP .

In this dissertation, several GA-based approaches for fractal image compression and active contour model are proposed. The main drawback of the classical fractal image compression is the long encoding time. Two methods are proposed in this dissertation to solve this problem. First, a schema genetic algorithm (SGA), in which the Schema Theorem is embedded in GA, is proposed to reduce the encoding time. In SGA, the genetic operators are adapted according to the Schema Theorem in the evolutionary process performed on the range blocks. We find that such a method can indeed speedup the encoder and also preserve the image quality. Moreover, based on the self-similarity characteristic of the natural image, a spatial correlation genetic algorithm (SC-GA) is proposed to further reduce the encoding time. There are two stages in the SC-GA method. The first stage makes use of spatial correlations in images for both the domain pool and the range pool to exploit local optima. The second stage is operated on the whole image to explore more adequate similarities if the local optima are not satisfactory. Thus not only the encoding speed is accelerated further, but also the higher compression ratio is achieved, because the search space is limited relative to the positions of the previously matched blocks, fewer bits are required to record the offset of the domain block instead of the absolute position. The experimental results of comparing the two methods with the full search, traditional GA, and other GA search methods are provided to demonstrate that they can indeed reduce the encoding time substantially. The main drawback of the traditional active contour model (ACM) for extracting the contour of a given object is that the snake cannot converge to the concave region of the object under consideration. An improved ACM algorithm is proposed in this dissertation to solve this problem. The algorithm is composed of two stages. In the first stage, the ACM with traditional energy function guides the snake to converge to the object boundary except the concave regions. In the second stage, for the control points which stay outside the concave regions, a proper energy template are chosen and are added in the external energy. The modified energy function is applied so as to move the snake toward the concave regions. Therefore, the object of interest can be completely extracted. The experimental results show that, by using this method, the snake can indeed completely extract the boundary of the given object, while the extra cost is very low. In addition, for the problem that the snake cannot precisely extract the object contour when the number of the control points on the snake is not enough, a GA-based ACM algorithm is presented to deal with such a problem. First the improved ACM algorithm is used to guide the snake to approximately extract the object boundary. By utilizing the evolutionary strategy of GA, we attempt to extract precisely the object boundary by adding a few control points into the snake. Similarly, some experimental results are provided to show the performance of the method.