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Computational biology enabled us to manage vast amount of experimental data and make inferences on observations that we had not made. Among the many methods, predicting metabolic functions with genome-scale models had shown promising results in the recent years. Using sophisticated algorithms, such as flux balance analysis, OptKnock, and OptForce, we can predict flux distributions and design metabolic engineering strategies at a greater efficiency. The caveat of these current methods is the accuracy of the predictions. We proposed using flux balance analysis with flux ratios as a possible solution to improving the accuracy of the conventional methods. To examine the accuracy of our approach, we implemented flux balance analyses with flux ratios in five publicly available genome-scale models of five different organisms, including Arabidopsis thaliana, yeast, cyanobacteria, Escherichia coli, and Clostridium acetobutylicum, using published metabolic engineering strategies for improving product yields in these organisms. We examined the limitations of the published strategies, searched for possible improvements, and evaluated the impact of these strategies on growth and product yields. The flux balance analysis with flux ratio method requires a prior knowledge on the critical regions of the metabolic network where altering flux ratios can have significant impact on flux redistribution. Thus, we further developed the reverse flux balance analysis with flux ratio algorithm as a possible solution to automatically identify these critical regions and suggest metabolic engineering strategies. We examined the accuracy of this algorithm using an Arabidopsis genome-scale model and found consistency in the prediction with our experimental data. / Master of Science

<p> The mechanisms operating during the metal-assisted growth of III-V nanowires (NWs) by molecular beam epitaxy on (1 1 l)B substrates were investigated through a series of experiments aimed at determining the influence of growth conditions on the morphology and crystal structure. Using GaAs as the principal material system for these studies, it is shown that a good control of these two characteristics can be achieved via a tight control of the temperature, V /III flux ratio, and Ga flux. Low and intermediate growth temperatures of 400°C and 500°C resulted in a strongly tapered morphology, with stacking faults occurring at an average rate of 0.1 nm^(-1). NWs with uniform diameter and the occurrence of crystal defects reduced by more than an order of magnitude were achieved at 600°C, a V /III flux ratio of 2.3, and a Ga impingement rate on the surface of 0.07 nm/s, and suggest the axial growth is group V limited. Increasing the flux ratio favored uniform sidewall growth, thus making the process suitable for the fabrication of core-shell structures. Further observation of steps on the sidewall surface of strongly tapered NWs suggests that radial growth of the shell proceeds in a layer-by-layer fashion, with the edge progressing in a step-flow mode toward the tip. </p> <p> From the experimental considerations, an analytical description of the growth is proposed, based on a simple material conservation model. Direct impingement of growth species on the particle, coupled to their diffusion from the sidewall and the substrate surface, are considered in the derivation of expressions for the time evolution of both axial and radial growths. Factors that take into account the nonunity probability of inclusion of group III adatoms in the axially growing crystal are introduced. Moreover, a step-mediated growth is included to describe the axial evolution of the shell. </p> / Thesis / Doctor of Philosophy (PhD)