Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1991. / Includes bibliographical references (leaves 344-358). / by Gareth Huw McKinley. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1994. / Includes bibliographical references (leaves 78-88). / by David M. Stevenson. / M.S.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2010. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / Polyhydroxyalkanoates (PHAs) are carbon storage polymers produced by a variety of bacteria. The model organism for studying PHA synthesis and accumulation is Ralstonia eutropha. This species can be used to convert renewable resources into PHA bioplastics, which can serve as biodegradable alternatives to traditional petrochemical plastics. A promising feedstock for PHA production is palm oil, a major agricultural product in Southeast Asia. Strains of R. eutropha were engineered to accumulate high levels of a PHA copolymer containing 3-hydroxybutyrate and 3-hydroxyhexanoate when grown on palm oil and other plant oils. This type of PHA has mechanical properties similar to those of common petrochemical plastics. The engineered strains expressed a PHA synthase gene from the bacterial species Rhodococcus aetherivorans I24. The amount of 3-hydroxyhexanoate in the PHA was controlled by modulating the level of acetoacetyl-CoA reductase (PhaB) activity in the engineered R. eutropha strains. Whole genome microarray studies were carried out to better understand R. eutropha gene expression during growth on plant oils. These results have provided insights that will allow for additional improvements to be made to the engineered strains. In order to study growth of R. eutropha strains on plant oils, fermentation methods were developed to grow the bacteria in oil medium and measure consumption of the carbon source. In one of these methods, the glycoprotein gum arabic was used to emulsify the plant oil. This emulsification reduced the lag phase in oil cultures and allowed representative samples to be taken early in experiments. High density palm oil fermentations were also carried out using unemulsified oil, which is more representative of industrial culture conditions. Techniques were developed for recovery of poly(3- hydroxybutyrate-co-3-hydroxyhexanoate) from R. eutropha biomass. Methyl isobutyl ketone was used to extract the PHA, and the polymer was precipitated from solution by addition of an alkane. A process model based on this procedure was developed for continuous recovery of PHA. The results described in this thesis include several advancements towards the goal of industrial PHA production from palm oil. / by Charles Forrester Budde. / Sc.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1931. / Includes bibliographical references (leaf 51). / by Paul V. Bitzer, Maurice W. Mayer. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1992. / Includes bibliographical references (leaves 164-171). / by Atsushi Edward Osawa. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 369-377). / Nonsmoothness in dynamic process models can hinder conventional methods for simulation, sensitivity analysis, and optimization, and can be introduced, for example, by transitions in flow regime or thermodynamic phase, or through discrete changes in the operating mode of a process. While dedicated numerical methods exist for nonsmooth problems, these methods require generalized derivative information that can be difficult to furnish. This thesis presents some of the first automatable methods for computing these generalized derivatives. Firstly, Nesterov's lexicographic derivatives are shown to be elements of the plenary hull of Clarke's generalized Jacobian whenever they exist. Lexicographic derivatives thus provide useful local sensitivity information for use in numerical methods for nonsmooth problems. A vector forward mode of automatic differentiation is developed and implemented to evaluate lexicographic derivatives for finite compositions of simple lexicographically smooth functions, including the standard arithmetic operations, trigonometric functions, exp / log, piecewise differentiable functions such as the absolute-value function, and other nonsmooth functions such as the Euclidean norm. This method is accurate, automatable, and computationally inexpensive. Next, given a parametric ordinary differential equation (ODE) with a lexicographically smooth right-hand side function, parametric lexicographic derivatives of a solution trajectory are described in terms of the unique solution of a certain auxiliary ODE. A numerical method is developed and implemented to solve this auxiliary ODE, when the right-hand side function for the original ODE is a composition of absolute-value functions and analytic functions. Computationally tractable sufficient conditions are also presented for differentiability of the original ODE solution with respect to system parameters. Sufficient conditions are developed under which local inverse and implicit functions are lexicographically smooth. These conditions are combined with the results above to describe parametric lexicographic derivatives for certain hybrid discrete/ continuous systems, including some systems whose discrete mode trajectories change when parameters are perturbed. Lastly, to eliminate a particular source of nonsmoothness, a variant of McCormick's convex relaxation scheme is developed and implemented for use in global optimization methods. This variant produces twice-continuously differentiable convex underestimators for composite functions, while retaining the advantageous computational properties of McCormick's original scheme. Gradients are readily computed for these underestimators using automatic differentiation. / by Kamil Ahmad Khan. / Ph. D.

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 21-27). / HIV infection has become a persistent worldwide epidemic despite the continuous development of novel inhibitors. A key challenge in combating HIV and other pandemic viral infections is the ability of the virus to mutate at an enormous rate and rapidly develop resistance to existing drugs. Among the various strategies that have been explored for the design of broadly binding HIV protease inhibitors, the substrate envelope hypothesis which is based on the idea of designing drugs that mimic the structural features of substrates has proved particularly effective. However, studies aimed at probing the substrate envelope hypothesis have found that the substrate envelope is a contributory but not sufficient property for robust binding and hence it is important to develop a better understanding of the other factors that contribute to binding promiscuity. This study investigated the key features which differentiate robust HIV protease inhibitors from susceptible HIV protease inhibitors by examining the interactions of certain known flat and nonflat binders with the different residues of HIV protease in terms of binding energy and number of contacts and correlating this analysis with the information about the mutational space of the virus. It was found that the promiscuous inhibitors, susceptible inhibitors and substrates all interact with the same set of HIV protease residues, some of which are vulnerable to primary mutations. The total contribution to the binding of an inhibitor/substrate to HIV protease from the HIV protease residues that are associated with primary mutations was observed to be a vital attribute separating flat binders from susceptible binders, with a greater contribution to binding from these residues translating into a higher susceptibility of the inhibitor to primary mutations. Certain strategies were proposed for incorporating these inferences in the computational drug design framework in order to generate robust HIV protease inhibitors. Although the analysis in this project was carried out using HIV protease as the model system, it is envisaged that the results obtained here would be generalizable to other rapidly mutating targets and hence these insights would facilitate drug design in the case of the outbreak of new epidemics of highly mutable infectious agents. / by Ishan Arora. / S.M.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1961. / Vita. / Includes bibliographical references (leaves 266-274). / by Arie Ram. / Sc.D.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1967. / Bibliography: leaves 160-164. / by William W. Cooper. / Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2004. / Includes bibliographical references. / Supervised by The need to eliminate hazardous solvents, such as methanol, toluene, and dichloromethane, in specialty and pharmaceutical chemical synthesis applications has motivated the development of alternative approaches. Because of its environmental compatibility, low cost, and favorable physicochemical properties, supercritical carbon dioxide (scCO2) has been actively considered to replace conventional hydrocarbon solvents. Progress towards this objective has been impressive, for example scCO2 is used as a selective extraction solvent in several commercial processes. By comparison, development of scCO2 as a reaction solvent has been much less successful due to its limited solvation power. Furthermore, the rates of reactions conducted in scCO2 tend to be slower than and their selectivities are comparable to those observed in hydrocarbon solvents. This research focused on development of water/carbon dioxide biphasic reaction systems as an engineering solution to increase reaction rates and manipulate selectivity while preserving environmental compatibility of scCO2. Emulsification by power ultrasound was selected as an additive-free means to bring near-critical liquid carbon dioxide and water into intimate contact and increase interphase transport. With this approach, the complementary solvation powers of the two solvents could be utilized to expand the range of potential chemical transformations. Carbon dioxide was envisioned as a delivery solvent, allowing access to the unique abilities of water to accelerate organic reactions while influencing their product spectrum. First, the partitioning behavior of organic solutes was investigated with the objective of developing empirical correlations for estimating partition coefficients. / (cont.) The available literature database was limited primarily to substituted phenols. This study nearly doubled the number of compounds for which carbon dioxide/water partition coefficient data are known to include a wider range of aromatic, aliphatic, and heterocyclic compounds. Several existing correlation methods, including a comparison to water solubility, estimation using octanol/water partition coefficients, and estimation using linear solvation energy relationships, were used. Good correlations were found using water solubility and octanol/water partition coefficients (0.4 log1o mole fraction units), provided that compounds with hydrogen bond donating ability were excluded from the analysis. A linear solvation energy relationship with optimized coefficients was found to accurately predict partition coefficients within ±0.2 log1o mole fraction units and was not limited to compounds that lack hydrogen bond donating ability. In general, such correlations should be useful for screening chemical reactions and for developing reactor designs. Power ultrasound at a frequency of 20 kHz was used to generate emulsions containing liquid, near-critical carbon dioxide and water. Since no surfactants were used, sonication simultaneously generated emulsions with water and carbon dioxide continuous phases. Visual observation and turbidity measurements indicated that all types of emulsions broke spontaneously within 30 minutes. The short lifetimes of these surfactant-free emulsions is expected ... / by Michael T. Timko. / Ph.D.