Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2003. / Includes bibliographical references (leaves 230-243). / Endogenous synthesis of nitric oxide (NO) is essential for many physiological functions, including the immune defense. However, the sustained, high production of NO by immune cells (macrophages) that accompanies chronic inflammation may be cytotoxic, mutagenic and carcinogenic. To better understand the roles of NO and its various reactive derivatives (e.g., N203 and ONOO-) in cancer, it is important to know the NO concentration and the total NO dose that tissue cells are exposed to during inflammation. To obtain this quantitative information, methods are needed for exposing cells to physiological levels of NO and its derivatives over relatively long periods of time. This research has therefore focused on developing in vitro delivery systems that mimic the in vivo release of NO. To permit continuous NO exposures over lengthy periods, an apparatus was fabricated which utilizes gas-permeable polydimethylsiloxane tubing to supply both NO and 02 to a stirred, cylindrical vessel. Mass transfer in this system was characterized by measuring the delivery rates of NO or 02 alone, and of NO to air-saturated solutions. It was found that the total flux of nitrogen species into the liquid was 40-90% greater in the presence of 02, depending on the NO partial pressure in the gas. Also, the simultaneously measured mass transfer coefficients for NO and 02 differed greatly from the corresponding unreactive values. An analysis of the data using diffusion-reaction models showed that NO oxidation in the aqueous boundary layer contributed very little to the nitrogen flux increase or to variations in the mass transfer coefficients. However, the unusually strong dependence of the delivery rates on chemical reactions could be explained by postulating that partial oxidation of NO to NO2 occurred within the membrane, with a rate constant of ... / (cont.) Using the measured mass transfer coefficients, the aqueous NO concentrations could be accurately predicted for the case of simultaneous NO and 02 delivery. The NO delivery system was used first to study the kinetics of plasmid DNA base deamination under pathologically relevant conditions. Three nucleobase products, 2'- deoxyxanthosine (dX), 2'-deoxyinosine (dI), and 2'-deoxyuridine (dU), were formed from 2'- deoxyguanosine (dG), 2'-deoxyadenosine (dA), and 2'-deoxycytosine (dC), respectively, at constant rates under steady state concentrations of 1.2 tM NO and 190 !pM 02. Morpholine nitrosation rates were measured under similar exposure conditions. Using a kinetic model, along with the known morpholine deamination kinetics, the three rate constants for base deamination were found to be nearly identical ... The second application of the new NO delivery system was to study NO-mediated cyto- and genotoxicity in two human lymphoblastoid cell lines, TK6 (wild-type p53) and NH32 (p53-null but isogenic to TK6). The TK6 and NH32 cells were each exposed to several steady-state NO concentrations for varying lengths of time, so that the total dose (area under the concentration-time curve) covered a wide range. Endpoint assays, including lethality, apoptosis, mitochondrial damage, and mutation rate in the thymidine kinase (TK1) gene locus, were performed at different post-treatment times ... / by Chen Wang. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005. / Includes bibliographical references (p. 175-188). / This thesis was motivated by the practical need to develop a scalable and cost-effective separation method for low-cost, high-volume protein products. This unmet challenge can potentially be addressed by extraction in two-phase aqueous micellar systems, in which biomolecules can be partitioned in mild, predominantly aqueous environments. The goal of this thesis was to explore various ways of enhancing protein partitioning in two-phase aqueous micellar systems, by the incorporation of electrostatic and affinity interactions, to obtain satisfactory yield and specificity for the purification of industrially relevant hydrophilic proteins. The electrostatically-enhanced partitioning of the enzyme glucose-6-phosphate dehydrogenase (G6PD) in two-phase aqueous mixed (nonionic/cationic) micellar systems was investigated experimentally and theoretically. The successful enhancement, up to 22-fold, of the partitioning of the negatively-charged G6PD was attained by adding the positively- charged surfactant alkyltrimethylammonium bromide (CnTAB) to form charged mixed micelles with the phase-forming nonionic surfactant, decyl tetra(ethylene oxide) (C₁₀E₄). / (cont.) The effects of the tail length of the positively-charged surfactant on protein denaturation and protein partitioning behavior were also studied. Furthermore, the experimental results were used to validate a predictive theory for electrostatic enhancement. In the area of affinity enhancement, the affinity-enhanced partitioning of an engineered affinity-tagged protein, CBM9-GFP (Green Fluorescent Protein linked to a carbohydrate- binding module), in two-phase aqueous micellar systems was investigated experimentally and theoretically. The experimental results showed that the partition coefficient of the target protein, CBM9-GFP, can be improved more than 6-fold, by virtue of the affinity interactions, and that the enhancement is specific to the target protein. The system utilized requires only one surfactant, decyl [beta]-D-glucopyranoside (C₁₀G₁), which acts simultaneously as the affinity ligand and as the phase-forming surfactant, and as such, has important practical advantages. A novel theoretical framework to describe affinity- enhanced protein partitioning in two-phase aqueous micellar systems was developed and validated experimentally. In addition, the separation method developed was successfully applied to a real cell lysate. / (cont.) It was found that the protein impurities in the cell lysate do not interfere with the partitioning of the target protein (CBM9-GFP) at industrially relevant concentrations, and that the protein impurities were concentrated away from the target protein. Lastly, the theoretical description developed was used to identify various strategies for improving the affinity-enhanced partitioning of the target protein in two-phase aqueous micellar systems. Although more work remains to be done before the separation methods studied in this thesis can reach their full potential and be eventually commercialized, this thesis nevertheless represents an essential starting point for future efforts to improve, extend, and commercialize this promising bioseparation method. / by Hei Ning Henry Lam. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 96-104). / DNA vaccines and gene therapies that use plasmid DNA (pDNA) as a vector have gained attention in recent years for their good safety profile, ease of manufacturing, and potential to treat a host of diseases. With this interest comes increased demand for high-yield manufacturing processes. Overall, this thesis aims to develop new, innovative tools for the production of plasmid DNA biopharmaceuticals. As one part of this thesis, we designed a 1-mL fed-batch microbioreactor with online monitoring and control of dissolved oxygen, pH, and temperature, as well as continuous monitoring of cell density. We used the microbioreactors to scale down temperature-induced production of a pUC-based DNA vaccine vector, pVAX1-GFP. Scaled-down processes can facilitate high-thoughtput, low-cost bioprocess development. We found that the microbioreactors accurately reproduced the behavior of a bench-scale bioreactor as long as key process parameters, such as dissolved oxygen, were held constant across scales. The monitoring capabilities of the microbioreactors also provided enhanced process insight and helped identify conditions that favored plasmid amplification. A second aspect of this thesis involved construction and characterization of a new DNA vaccine vector based on a runaway replication mutant of the R1 replicon. Runaway replication plasmids typically show increased amplification after a temperature upshift. However, we found that our new vector, pDMB02-GFP, gave higher yields during constant temperature culture at 30"C, reaching a maximum of 19 mg pDNA/g DCW in shake flasks. We gained mechanistic insight into this behavior by measuring RNA and protein expression levels of RepA, a plasmid-encoded protein required for initiation of replication at the R1 origin. Through these studies we found that RepA levels may limit plasmid amplification at 42*C, and relieved this limitation by increasing RepA translation efficiency via a start codon mutation. We also scaled up production of pDMB02-GFP at 300C from 50-mL shake flasks to 2-L bioreactors. Initial scale up efforts resulted in increased growth rate compared to the shake flasks, accompanied by very low plasmid yields. Decreasing the growth rate by limiting dissolved oxygen increased plasmid specific yield and emerged as a viable strategy for maintaining productivity during scale up. / by Diana M. Bower. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2004. / Includes bibliographical references (p. 180-195). / (cont.) approaches to improving hepatocyte function in culture have been described, not all of the important functions--specifically the biotransformation functions of the liver--can as yet be replicated at desired in ivo levels, especially in culture formats amenable to routine use in drug development. The in vivo microenvironment of hepatocytes in the liver capillary bed includes signaling mechanisms mediated by cell-cell and cell-matrix interactions, soluble factors, and mechanical forces. This thesis focuses on the design, fabrication, modeling and characterization of a microfabricated bioreactor system that attempts to mimic the in vivo microenvironment by allowing for the three dimensional morphogenesis of liver tissue under continuous perfusion conditions. A key feature of the bioreactor that was designed is the distribution of cells into many tiny ([approximately]0.001 cm³) tissue units that are uniformly perfused with culture medium. The total mass of tissue in the system is readily adjusted for applications requiring only a few thousand cells to those requiring over a million cells by keeping the microenvironment the same and scaling the total number of tissue units in the reactor. Using a computational fluid dynamic model in ADINA® and a species conservation mass transfer model in FEMLAB®, the design of the bioreactor and the fluidic circuit was optimized to mimic physiological shear stress rates ... / Recent reports indicate that it takes nearly $800 million dollars and 10-15 years of development time to bring a drug to market. The pre-clinical stage of the drug development process includes a panel of screens with in vitro models followed by comprehensive studies in animals to make quantitative and qualitative predictions of the main pharmacodynamic, pharmacokinetic, and toxicological properties of the candidate drug. Nearly 90% of the lead candidates identified by current in vitro screens fail to become drugs. Among lead compounds that progress to Phase I clinical trials, more than 50% fail due to unforeseen human liver toxicity and bioavailability issues. Clearly, better methods are needed to predict human responses to drugs. The liver is the most important site of drug metabolism and a variety of ex vivo and in vitro model systems have therefore been developed to mimic key aspects of the in vivo biotransformation pathways of human liver-- a pre-requisite for a good, predictive pharmacologically relevant screen. Drug metabolism or biotransformation in the liver involves a set of Phase I (or p450 mediated) and Phase II enzyme reactions that affect the overall therapeutic and toxic profile of a drug. The liver is also a key site of drug toxicity following biotransformation, a response that is desirable but difficult to mimic in vitro. A major barrier to predictive liver metabolism and toxicology is the rapid (hours) loss of liver-specific functions in isolated hepatocytes when maintained under standard in itrom cell culture condition. This loss of function may be especially important in predicting toxicology, where the time scale for toxic response may greatly exceed the time scale for loss of hepatocyte function in culture. Although a wide variety of / by Anand Sivaraman. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1995. / Includes bibliographical references (p. 55-60). / M.S.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1952. / Vita. / Includes bibliographical references (leaves 203-208). / by Hyman Resnick. / Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2001. / Includes bibliographical references (p. 237-251). / Advances in MEMS (micro-electromechanical systems) have enabled some of the "Lab-on-a-Chip" technologies and microfluidics that are pervasive in many of the current developments in analytical chemistry and molecular biology. Coinciding with this effort in micro-analytics has been research in chemical process miniaturization -- reducing the characteristic length scale of the unit operation to improve heat and mass transfer, and ultimately process performance. My research has involved the design and fabrication of novel chemical reaction systems using MEMS and microfabrication methods (photolithography, deep-reactive-ion etching, thin-film growth and deposition, and multiple wafer bonding). Miniature chemical systems provide the opportunity for distributed, on-demand manufacturing, which would eliminate the hazards of transportation and storage of toxic or hazardous chemical intermediates. Reactions that are particularly suitable for miniaturized chemical systems are those that are fast and involve toxic intermediates: the controlled synthesis of phosgene is such a reaction and has been demonstrated in a microfabricated packed bed reactor. Owing to the high surface-to-volume ratios, micro chemical systems also have the potential to make improvements in process performance through enhanced heat and mass transfer. / (cont.) Heterogeneously catalyzed gas-liquid reactions have been performed in the microfabricated reactors and have been shown to have mass transfer coefficients several orders of magnitude larger than their industrial-scale counterparts. Multiphase reactions are often hindered by mass-transfer limitations owing to the difficulty in transporting the gaseous reactant through the liquid to the catalytic surface. The microchemical device has been designed to increase the interfacial gas-liquid contacting area by promoting dispersion and preventing coalescence. Microfabrication allows the design of reactors with complicated fluidic distribution networks, staggered arrays of microstructural features to promote mixing, and the integration of sensing and temperature control. Other uses of microfabrication include the incorporation of porous silicon as a high surface area catalyst support. In all, performing multiphase chemistry on a chip has been demonstrated to have inherent advantages, particularly for those fast reactions that can benefit from improved mixing and mass transfer. / by Matthew W. Losey. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Associating polymers have attracted much interest in a variety of applications such as selfhealing materials, biomaterials, rheological modifiers, and actuators. The interplay of polymer topology and sticker chemistry presents significant challenges in understanding the physics of associating polymers across a wide range of time and length scales. This thesis aims to provide new insights into the structure-dynamics-mechanics relationships of associating polymer networks. This thesis first examines diffusion of various types of associating polymers in the gel state through a combination of experiment and theory. By using forced Rayleigh scattering (FRS), phenomenological super-diffusion is revealed as a general feature in associating networks. Experimental findings are quantitatively explained by a simple two-state model that accounts for the interplay of chain diffusion and the dynamic association-dissociation equilibrium of polymer chains with surrounding network. Furthermore, hindered self-diffusion is shown to directly correlate with a deviation from the Maxwellian behavior in materials rheological response on the long time scale. To further understand how sticker dynamics affects the network mechanical properties, a new method referred to as "sticker diffusion and dissociation spectrometry" is developed to quantify the dissociation rate of stickers in the network junctions. It is demonstrated that sticker dissociation is a prerequisite step for sticker exchange that leads to macroscopic stress relaxation. Finally, this thesis explores the use of fluorescence recovery after photobleaching (FRAP) to measure self-diffusion of associating polymers, and a mathematical framework is established. The second part of this thesis focuses on the development of new methods of controlling the mechanical properties of associating networks through engineering the molecular structure of polymer chains. Specifically, topological entanglement is introduced into the network through extending the polymer chains to reach beyond their entanglement threshold. This strategy drastically enhances material's toughness, extensibility, creep resistance and stability in solutions. Various types of coupling chemistries are then explored to fine tune the extent of entanglement. The entanglement effect and the long-time relaxation of materials can be further controlled by introducing branching points into the macromolecules. / by Shengchang Tang. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2013. / 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 (pages 72-80). / Continuous flow systems for chemical synthesis have become increasingly important in the pharmaceutical and fine chemical industry in the past decade. Initially, this work was confined primarily to microfluidic systems, but recently there has been a growing demand for milliscale systems capable of making material for clinical trials and pilot plant testing. The objective of this thesis is to demonstrate a practical system to accomplish continuous chemical synthesis within the context of a fully integrated pilot plant. The plant provided a platform to test scaled-up membrane-based liquid-liquid separators which were studied in detail. Previous work demonstrated the use of microfiltration membranes to separate liquid-liquid systems by leveraging the dominance of interfacial tension over gravity at small scales. When scaling up, it was determined that pressure control was critical to the operation of the separators. A pressure control module was designed and integrated into the separator device to provide the appropriate conditions to guarantee separation. The separators required no outside control to accomplish separation when connected to various downstream conditions including pumps, backpressure controllers, and other separators. This allowed for easy design and operation of multistep processes such as solvent swaps and countercurrent extraction. The main accomplishment covered in this thesis is the building and operation of an integrated continuous manufacturing plant for a small molecule pharmaceutical product (aliskiren tablets). An advanced intermediate was continuously processed through two synthetic steps with workup which are detailed here. The remainder of the process purified and formulated the drug substance and formed the final tablet which met many key performance criteria. This work opens avenues to look at even more complex liquid-liquid and even gas-liquid separation processes. Improved processes for continuous manufacturing which make use of recycling, multistage extraction, and novel chemistries can build on the research performed here to further improve synthesis systems. These results demonstrate that continuous processes are possible even for complex, industrially-relevant products. / by Patrick Louis Heider. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, June 2017. / Cataloged from PDF version of thesis. "June 2017"--Handwritten on title page. / Includes bibliographical references. / In recent years, nanoparticles have demonstrated immense promise for the development of next generation technologies for subsurface reservoir characterization and oil recovery. Until now however, the scope of such nanoparticles has been limited due to the significant challenge of colloidal stabilization under the extreme salinity and high temperature conditions typical of a reservoir. Previous efforts to address this problem have focused on conventional polyelectrolyte based stabilizers, which unfortunately fail at high ionic strengths due to excessive charge screening. In this thesis, we demonstrate a new approach to stabilization that overcomes this key deficiency, by specifically taking advantage of the excessive charge screening afforded by high ionic strengths. The approach is based on the anti-polyelectrolyte phenomenon, in which screening of intra-chain electrostatic interactions causes a polyzwitterion to undergo a structural transition from a collapsed globule to a more open coil-like regime. We first fundamentally investigate the anti-polyelectrolyte phenomenon in a high density comb type polyzwitterion, poly(sulfobetaine methacrylamide) (polySBMA), via small angle neutron scattering. The phenomenon is probed at a range of molecular weights by utilizing low dispersity homopolymers synthesized via controlled radical polymerization methods. Unique non gaussian behavior with significant molecular weight dependencies of size and shape is observed. An electrostatic dependence for Kuhn length is also established. Subsequently, we extend our understanding of anti-polyelectrolyte systems by characterizing the conformational dependence of polySBMA under conditions such that its responsive swelling is confined due to the segments being bound in three, six and twelve armed star architectures. Chain stretching due to solid angle exclusion, as well as, strong dependencies of size and fractal dimension on electrolyte concentration, number of arms and degree of polymerization (per arm) are noted. After gaining a detailed insight of the anti-polyelectrolyte phenomenon, its unique osmotic response is engineered into electrolyte and temperature responsive polyzwitterionic stabilizers. Robust colloidal stability of silica and polystyrene nanoparticles under reservoir relevant conditions is demonstrated, and the design principles of developing colloidally stable nanoparticles are elucidated. Finally, the polyzwitterion functionalized nanoparticles are leveraged in the form of schizophrenic diblock copolymer functionalized nanoparticles, to develop temperature tunable pickering emulsifiers. In contrast to conventional temperature responsive pickering emulsifiers, which induce phase separation upon heating, the schizophrenic diblock copolymer functionalized nanoparticles are demonstrated to function in the reverse direction, by inducing demulsification upon cooling. The unique temperature response is noted to be cyclable, and is likely to render the particles of important utility in enhanced oil recovery demulsification. / by Mikhil Ajay Ranka. / Ph. D.