Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1968. / Vita. / Bibliography: leaves 252-257. / by Thomas A. Jadwin. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1987. / Bibliography: leaves 266-270. / by Joseph John Helble. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006. / Vita. / Includes bibliographical references (leaves 91-102). / Intracellular networks arise from complex interactions between proteins that relay signals and control cellular responses. Viruses, with limited genetic material, can modify network signals and change cell behavior. Replication-deficient viruses are used extensively as delivery vectors in clinical gene therapy and in molecular biology, but little is known about how the viral carrier itself contributes to cellular responses. In this thesis, we explored the link between viral vector modifications of signaling networks to changes in cellular phenotype. We approached this problem by studying a therapeutically relevant model in which an adenoviral vector (Adv) sensitizes human tumor epithelial cells to tumor necrosis factor (TNF)-induced apoptosis. We first measured TNF-stimulated signaling profiles over a range of Adv infection levels for a distribution of kinases centrally involved in the TNF signaling network. We then applied quantitative analytical techniques to determine the most important signals contributing to Adv-induced changes in TNF-mediated apoptosis. We experimentally derived a mathematical equation describing the saturation of anti-apoptotic Akt effector signaling in the presence of high levels of Adv infection, which could predict TNF-induced apoptosis in HT-29 cells. / (cont.) However, the same equation did not apply in HeLa cells, suggesting that one-signal models are insufficient to account for complex network interactions. Therefore, we applied a systems-modeling approach to our Adv-TNF system and mathematically identified a multivariate signal-processing function sufficient to predict Adv-TNF induced apoptosis in both HT-29 cells and HeLa cells. The common-processing model identified critical Adv-induced cell-specific signaling modifications, and accurately predicted apoptosis following perturbation with pharmacological inhibitors of Akt and IKK. Thus, by combining experimental and computational approaches, this thesis has identified an important biological principle, common signal processing, for studying cell-specific responses to viral infections and rational drug therapies. / by Kathryn E. Miller. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1988. / Includes bibliographical references. / by Craig Bryce Vaughn. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The nonlinear coupling between an exothermic chemical reaction and a nanowire or nanotube with large axial heat conduction guides a self-propagating thermal wave along the nano-conduit. The thermal conduit accelerates the wave by rapidly transporting energy to un-reacted fuel. The reaction wave induces what we term a thermopower wave, resulting in an electrical current in the same direction. At up to 7 W/g, peak power density is larger than that of many present micro-scale power sources (e.g. fuel cells, batteries) and even about seven times greater than commercial Li-ion batteries. Thermopower waves also tend to produce unipolar voltage pulses, although conventional thermoelectric theory predicts bipolar voltage. These waves also generate thermopower in excess of previous measurements in carbon nanotubes (CNTs) and therefore could increase figures of merit in a variety of thermoelectric materials. In this thesis, I have developed the theoretical framework to describe the thermal and chemical profiles of propagating reaction waves, and their electrical properties. My analysis yielded a new analytical solution for one-dimensional reaction and thermal diffusion systems with nth order kinetics that obviates many approximate or numerical approaches from the past 80 years. A generalized logistic. function describes the temperature and concentration profiles within the solid fuel and provides a solution for the wave velocity for a wide range of conditions. This approach offers new insight into such problems spanning several fields in science and engineering, including propulsion and self-propagating high temperature synthesis (SHS) of materials, as well as the dynamics of thermopower waves. Temperature and voltage measurements of thermopower waves on CNTs show that they can generate power as much as four times greater than predictions based on reference measurements of the Seebeck coefficient for static temperature gradients. We hypothesize that the excess thermopower stems from a chemical potential gradient across the CNTs. The fuel (e.g. picramide) adsorbs and dopes the CNTs ahead of the wave and desorbs and reacts behind the wave front. Furthermore, the excess thermopower depends on the mass of fuel added (relative to CNT mass), and the chemical potential difference matches the magnitude of the excess thermopower. Thus, a major conclusion of this thesis is that coupling to a chemical reaction can boost the performance of thermoelectric materials through differential doping. Thermopower waves can have well defined velocity oscillations for certain kinetic and thermal parameter values. Cyclotrimethylene-trinitramine (fuel) on multiwalled CNTs (conduit) system generates voltage oscillations of 400 to 5000 Hz. These frequencies agree with velocity oscillations predicted by my thermochemical model of the reaction wave, extended to include thermal transport within the conduits. Thermopower waves could thus find applications as new types of alternating current (AC) batteries and self-powered signal generators, which could easily be miniaturized. Microelectromechanical systems and sensors would benefit from thermopower wave generators to enable functions such as communications and acceleration that currently require large power packs. Additionally, the "self-discharge" rate of thermopower wave generators is extremely low in contrast to electrochemical storage, since their energy is stored in chemical bonds. Thermopower waves thus enable new energy storage devices and could exceed limitations of conventional thermoelectric devices. / by Joel T. Abrahamson. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1948. / Includes bibliographical references (leaf 68). / by P.V. Danckwerts, A.C. Sugden. / M.S.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2002. / Includes bibliographical references (p. 170-186). / Oxidation is one of the most prevalent forms of chemical modification, and the sulfur-containing amino acids, methionine and cysteine, are susceptible to modification by a wide array of oxidants. Aberrant oxidation reactions are of particular concern in biotechnology and medicine, where they can lead to protein inactivation or destabilization. Therefore, it is important to understand the factors that influence a protein's reactivity toward oxidants from both a bioprocessing and a biomedical perspective. This work characterizes oxidation of methionine and cysteine in recombinant human xcl-antitrypsin, a metastable protein that is a member of the serpin family of plasma protease inhibitors. Analytical techniques were developed to identify and quantify oxidation of each of al-antitrypsin's ten methionine residues, as well as its unpaired thiol, Cys232. It was found that the protein is not susceptible to oxidation during production in the E.coli cytoplasm, but does contain highly-reactive methionine and cysteine residues that are of considerable importance within the context of in vitro oxidation. At neutral pH, five methionines, Metl, Met226, Met242, Met351, and Met358, are reactive with hydrogen peroxide. With the exception of Metl, each of these residues is located in or near the protein's active site loop. Methionine oxidation studies revealed that the reactivity of these residues is dependent on environmental conditions, such as pH, that readily perturb the protein's metastable structure. / (cont.) Cys232 oxidation studies showed that oxidation of [alpha]l-antitrypsin's unpaired thiol does not lead to the formation of disulfide-linked aggregates, but rather sulfenic, sulfinic, and cysteic acids in successive steps. These species are rapidly formed in vitro as a consequence of Cys232's unusually low pKa of 6.86. Modulation of Cys232's ionization and reactivity could not be accomplished via low pH, however, due to acid-induced structural changes that enhance reactivity. In sum, analytical techniques were developed to study methionine and cysteine oxidation in [alpha]1-antitrypsin and it was found that elements of protein structure that have evolved for the physiological functioning of plasma protease inhibitors dictate oxidation susceptibility during bioprocessing and long-term storage. In the case of oxl-antitrypsin, and perhaps other proteins with similar structural biochemistries, unpaired-thiol oxidation, and not methionine oxidation, is the major contributor to oxidative degradation in vitro. / by Steven Wesley Griffiths. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016. / "February 2016." Page 102 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / With an increasing understanding of the molecular bases of disease, macromolecules such as proteins and siRNA can potentially be used as therapeutics, modulating biological function with high specificity to reverse pathological progression. However, while certain contexts require manipulating the biology inside the cell, the large size and charge of macromolecules prevent them from spontaneously crossing the cell membrane. For proteins, this problem limits the scope of diseases that are potentially addressable. For siRNA, this prevents access to the cellular machinery responsible for executing gene silencing in the first place. Thus, a safe and effective method to deliver proteins and siRNA into the cytoplasm is desired to fully enable their therapeutic potential. In this thesis, we describe the development of an intracellular delivery system based on a bacterial pore-forming protein, and demonstrate its efficacy in vitro using protein and siRNA payloads. Perfringolysin O (PFO) is a member of the cholesterol-dependent cytolysin (CDC) family of bacterial toxins whose pores, reaching up to 30nm in diameter, allow the passage of large molecules without a specialized transport mechanism. However, the creation of such pores on the cell membrane is accompanied by cytotoxicity, which limits the practical use of these proteins as a delivery tool. Thus, we developed a strategy to selectively activate PFO in endosomal compartments to minimize cytotoxicity. Specifically, we engineered a neutralizing binder against PFO on the fibronection scaffold. The binder was designed to have a higher affinity for PFO at neutral pH, inhibiting pore-formation on the cell membrane, and a lower affinity at acidic pH, promoting pore-formation on endosomal membranes. Fusing this binder to an antibody against EGFR allowed specific targeting and internalization. Using a protein payload-the ribosome-inactivating protein gelonin-administered in trans, we demonstrated that this strategy enables efficient delivery with high specificity and low toxicity, increasing the therapeutic window of PFO by orders of magnitude in vitro. One advantage of this delivery system is its modularity, as the payload administered in trans is readily swappable with other molecules of interest. Thus, we next demonstrated that the neutralized PFObased system can also be used for intracellular delivery of siRNA. For this application, we engineered a targeted siRNA carrier based on the dsRNA-binding protein p19 of the Carnation Italian Ringspot Virus (CIRV). In particular, we matured the affinity of p19 to create clones with some of the highest affinities for siRNA reported to date. Higher affinity correlated with higher potency, with the tightest-binding p19 mutant enabling silencing of a reporter gene with pM concentrations of siRNA in vitro. This increase in potency was partially due to increased uptake of siRNA. However, we also observed that the high-affinity clones enable stronger silencing even When each clone internalizes similar numbers of siRNA. This observation suggests that prolonging the association of siRNA and its carrier inside the cell may be a strategy for further improving the efficiency of silencing. Overall, the work described in this thesis demonstrates how neutralizing binders can be used to control the activity of potent membrane-disrupting agents, to deliver exogenous macromolecules into the cytoplasm with low toxicity. Further optimization of the neutralized PFO-based system for in vivo use will enhance its utility as a viable therapeutic strategy. / by Nicole J. Yang. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1988. / Includes bibliographical references (leaves 232-239). / by Glen H. Ko. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Supercritical Water (SCW) desulfurization was investigated for both model sulfur compounds and Arab Heavy crude. In part 1, the reactions of alkyl sulfides in SCW were studied. During hexyl sulfide decomposition in SCW, pentane and CO+CO₂ were detected in addition to the expected six-carbon products. A multi-step reaction sequence for hexyl sulfide reacting with SCW is proposed which explains the surprising products. Intermediate studies were performed to confirm that the key intermediate hexanal forms and rapidly decomposes to pentane and CO. In part 2, Arab Heavy crude was treated with SCW and analyzed with comprehensive gas chromatography (GCxGC) coupled with two detectors, sulfur chemiluminescence detector (SCD) and a flame ionization detector (FID). SCD is a sulfur specific detector that allowed detailed analysis of the reactions that occur during SCW treatment of real fuel mixtures. It was shown that SCW treatment had two effects on sulfur compounds: cracking of heavy sulfur compounds into smaller compounds, mainly benzothiophenes (BT) and dibenziophenes (DBT), and cracking of long alkyl chains on these BTs and DBTs causing a shift to lower molecular weight BTs and DBTs. SCW was found to be ineffective in breaking the stable aromatic rings of these thiophenic compounds. Work in this thesis shed light into molecular level reactions during SCW treatment rather than changes in bulk properties which are often reported in work in the field of SCW desulfurization. / by Yuko Kida. / Ph. D.