Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2000. / Includes bibliographical references (p. 367-387). / Microdefect formation in crystalline material is strongly correlated to the processing conditions for growth of crystals important in microelectronic processing. The geometry and operation conditions for crystal growth systems affect the temperature profile in the crystal and melt, which influences microdefect formation. The objectives of this thesis are to formulate the computational framework to establish the linkage between microdefect formation in crystal and proce5sing conditions of crystal growth system. The research focuses on two industrially important crystal growth problems: Czochralski (CZ) growth of single-crystal silicon and growth of bismuth germanium oxide (Bi4Ge30 12:BGO) by the vertical Bridgman method. A sequential, two-step approach is taken for linking mathematical modeling between processing conditions and microdefect formation in crystals. An accurate model of heat transfer in CZ growth of silicon is developed by including all the components in the system. Microdefoct formation in the crystal is then modEled by imposing the temperature profile obtained by the global heat transfer simulation. The integrated hydrodynamics thermal-capillary model (IHTCM) of CZ crystal growth includes radiative and conductive heat transfer between all components of the system. An important component of this simulation is the incorporation of a model of turbulence in the melt. A low Reynolds number k-c model is incorporated into the IHTCM for CZ system. The coupled k-c/IHTCM is applicable to any CZ system geometry and operating conditions because of the self-consistency of the model. Also a robust numerical solution method is developed to solve numerically unstable k-c equations by a finite-element approximation. The comparison between simulations and experiments for CZ growth of an 8" diameter crystal shows semi-quantitative agreement in melt/crystal interface, oxygen concentration in the crystal, and the location of a neutral zone, where the concentrations of two intrinsic point defects balance, in the crystal. Microdefect formation in CZ silicon is modeled with intrinsic point defects (vacancies and self-interstitials) and their agglomerates. The model is two-dimensional in space and predicts the radial profiles of point defects, which are determined near the melt/crystal interface, and the axial development of size distribution of voids and self-interstitial agglomerates, which is a function of point defect supersaturation and the temperature profile. The model provides quantitative links between operating conditions and microdefect distribution in the entire crystal. An effective numerical method with parallel processing is developed using a mixed local discontinuous Galerkin method. The predicted agglomeration temperatures and densities for vacancy and self-interstitial clusters are within the ranges of experimental data. The predictions also include the location for ring-like oxidation-induced stacking fault (OSF) formation, assuming the OSF-ring is formed at the radial location with the peak in residual vacancy concentration after the onset of vacancy agglomeration. The simulations clearly reproduce the radial distribution of microdefects observed by experiments. Starting from the crystal center and moving to the edge, the simulations predict a void region, the OSF-ring as a region of locally high vacancy concentration, a defect free region, a region dominated by self-interstitial clusters, and finally a defect free region near the crystal edge. The defect free region at the crystal edge results from the radial diffusion of point defects caused by reactions at the crystal surface. The heat transfer model in the vertical Bridgman system for BGO crystal growth incorporates internal radiation in the semi-transparent BGO crystal and conduction and radiation for all components of the heat transfer system. A band approximation is used to model internal radiation in the crystal. The global heat transfer model provides quantitative understanding of the heat transfer within the semi-transparent BGO crystal as well as in the entire system. Comparison of the temperature profile at the crucible wall between simulations and experiments for the large 11 cm diameter BGO crystal growth shows good agreement. The detailed analysis of heat transfer near the solidification interface gives insight for the control of bubble defects in BGO crystal formed by constitutional supercooling. The framework for numerical simulations developed in this thesis quantitatively demonstrates the linkage between processing conditions and microdefect formation in crystalline material. The linkage is established by the coupling of self-consistent modeling of global heat transfer in the crystal growth systems and microdefect formation in crystals. / by Tatsuo Mori. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1995. / Includes bibliographical references (leaves 152-168). / by Henry Raymond Costantino, Jr. / Ph.D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1943. / MIT copy bound with: Characteristics of turbulent flames / George Feick, III, Robert Miller Greene, Jr., Eduardo F. Herrerías. 1943. / Includes bibliographical references (leaf 36). / by Raymond F. Frankel, Jr., Simon E. Gluck, Robert H. Handler, Christian J. Matthew. / B.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1985. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Bibliography: leaves 254-256. / by Saad Akhtar Khan. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Vita. / Includes bibliographical references (leaves 128-134). / Huntington's Disease (HD) is an autosomal dominant neurodegenerative disorder caused by an expansion in the number of polyglutamine-encoding CAG repeats in the gene that encodes the huntingtin (htt) protein. A property of the mutant protein that is intimately involved in the development of the disease is the propensity of an N-terminal proteolytic htt fragment containing the glutamine-expanded region to misfold and adopt a conformation which is prone to aggregation. Intracellular antibodies (intrabodies) against htt have been shown to reduce htt aggregation by binding to the htt fragment and inactivating it or preventing its misfolding. Intrabodies may therefore be a useful gene therapy approach to treatment of the disease. However, high expression levels of previously reported intrabodies have been required to obtain even limited reductions in htt aggregation. We have used yeast surface display (YSD) of antibodies combined with fluorescence activated cell sorting (FACS) to isolate novel single-chain antibody (scFv) clones against huntingtin from a non-immune human antibody library; these scFv's did not inhibit htt aggregation. Engineering analysis, including the derivation of equations that describe the probability that cells will form htt aggregates as a function of time and concentration, were used to estimate the intracellular expression level and binding affinity required for robust aggregation inhibition. / (cont.) The pool of antibodies isolated was used as the starting point for engineering an intrabody with appropriate properties for intracellular activity. We then applied YSD to affinity mature this scFv pool for binding to the first 17 aa of htt and analyze the location of the binding site of the intrabody mutant with the highest affinity. Interestingly, the paratope was mapped exclusively to the variable light chain domain of the scFv. A single domain antibody was constructed consisting solely of this variable light chain domain, and was found to retain full binding activity to huntingtin. Cytoplasmic expression levels of the single domain were at least five-fold higher than the scFv, enabling mild aggregation inhibition. However, antibodies expressed in the cytoplasm do not form intradomain disulfide bonds as they do when secreted from cells. By mutating the cysteine residues that form the disulfide bond in the single-domain antibody to hydrophobic amino acids, we found that antibody binding affinity was drastically reduced in the absence of the disulfide bond. Effectiveness of the single-domain intrabody was improved by increasing its affinity in the absence of a disulfide bond. The engineered intrabody, VL12.3, eliminated toxicity in a neuronal model of HD. We also found that VL12.3 inhibited aggregation and toxicity in a S. cerevisiae model of HD. VL12.3 is significantly more efficient than earlier anti-htt intrabodies, and is a potential candidate for gene therapy treatment for HD. / (cont.) The approach demonstrated to improve intrabody potency through the use of highly expressed single-domain antibody fragments and disulfide bond-independent binding suggests a generally applicable approach to the development of effective intrabodies against other intracellular targets. / by David W. Colby. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 290-299). / Continuous manufacturing offers a number of operational and financial benefits to pharmaceutical companies. This research examines the critical blending step for continuous pharmaceutical manufacturing and the characteristics of continuous downstream pharmaceutical manufacturing systems. Discrete element method (DEM) simulations were used to develop novel insights into the mechanism of mixing for continuous blending of cohesive pharmaceutical powders and to examine the effects of particle properties, blender design and operating conditions on blend homogeneity. To place continuous blending into the context of pharmaceutical manufacturing, the scope of the analysis was expanded to process system models of continuous downstream pharmaceutical manufacturing. DEM simulations were used to study the mechanisms of mixing in the continuous blending of pharmaceutical powders. Diffusive mixing from the avalanching particles appears to be the dominant mechanism of mixing in both the axial and radial direction for the double helical ribbon blender. This result can guide the development of future continuous pharmaceutical powder blenders by optimizing the mixing elements to increase the amount of particles transported to a position where they can avalanche/flow and diffusively mix. A range of particle properties, blender designs and operating conditions were examined for their effects on flow behavior and blend homogeneity. Three particle properties were examined: particle size, polydispersity and cohesive force. / (cont.) Particle size was observed to be positively correlated to both flow rates and blend homogeneity. Polydispersity had no effect on flow rate and was negatively correlated to homogeneity. Cohesive force was negatively correlated to flow rate and had little to no effect on homogeneity. Two modifications of blender design were analyzed: changes in blender size and changes in shaft design. Blender size was observed to be positively correlated to flow rate and negatively correlated to homogeneity. The paddle shaft designs created a more homogeneous powder blend than the double helical ribbon shaft. Two operating parameters were also studied: rotation rate and fill fraction. Rotation rate was positively correlated to both flow rate and homogeneity. Fill fraction had the interesting result of being positively correlated to the absolute flow rate, but negatively correlated to the fill mass normalized flow rate. In addition, fill fraction has a clear negative correlation to homogeneity above fill fractions of 0.55, but is inconsistent for fill fractions lower than this. This research on particle properties, blender designs and operating conditions will help to guide the operation of continuous pharmaceutical blenders and the design of continuous pharmaceutical manufacturing systems. Process simulations comparing model batch and continuous downstream pharmaceutical manufacturing systems have quantified some of the potential size, cost and performance benefits of continuous processes. The models showed significant reductions in process equipment sizes for continuous manufacturing particularly in the blending step. / (cont.) This reduction in equipment size translates to capital cost (CAPEX) savings for both the continuous process equipment and manufacturing facilities. The steady state operation of continuous processing also reduces the labor requirements and gives the continuous processes an operating cost (OPEX) advantage over batch processes. This research has contributed to the understanding of continuous pharmaceutical powder blending and quantified some of the benefits of continuous downstream pharmaceutical manufacturing. This work is being continued by the Novartis-MIT Center for Continuous Manufacturing whose work is providing the foundation for future industrial scale pharmaceutical continuous manufacturing systems. / by Matthew J. Abel. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013. / Cataloged from PDF version of thesis. "December 2012." / Includes bibliographical references (p. 234-249). / We first reported the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT) 15 oligonucleotides, adsorbed to an array of near infrared fluorescent semiconducting single-walled carbon nanotubes (AT₁₅-SWCNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)₁₅ imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol, enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT₁₅ - SWCNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWCNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in estimation is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-SWCNT-site NO adsorption rate constant is 0.001 s-¹ [mu]M NO-¹. The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation. Further, we also explored the concept of creating molecular recognition sites using polymer-SWCNT complexes. Molecular recognition is central to the design of therapeutics, chemical catalysis and sensor platforms, with the most common mechanisms involving biological structures such as antibodies[l] and aptamers[2, 3]. The key to this molecular recognition is a folded and constrained heteropolymer pinned, via intra-molecular forces, into a unique three-dimensional orientation that creates a binding pocket or interface to recognize a specific molecule. An alternate approach to constraining a polymer in three-dimensional space involves adsorbing it onto a cylindrical nanotube surface[4-7]. To date, however, the molecular recognition potential of these structured, nanotube-associated complexes has been unexplored. In this work, we demonstrate three distinct examples in which synthetic polymers create unique and highly selective molecular recognition sites once adsorbed onto a single-walled carbon nanotube (SWCNT) surface. The phenomenon is shown to be generic, with new recognition complexes demonstrated for riboflavin, L-thyroxine, and estradiol, predicted using a 2D thermodynamic model of surface interactions. The dissociation constants are continuously tunable by perturbing the chemical structure of the heteropolymer. The complexes can be used as new types of sensors based on modulation of SWCNT photoemission, as demonstrated using a complex for real time spatio-temporal detection of riboflavin in murine macrophages. Cardiac biomarkers troponin I and T are recognized as standard indicators for acute myocardial infarction (AMI, or heart attack), a condition that comprises 10% of U.S. emergency room visits [8]. There is significant interest in a rapid, point-of-cae (POC) device for troponin detection[9]. In this work we demonstrate a rapid, quantitative, and label-free assay specific for cardiac troponin T detection, using fluorescent single-walled carbon nanotubes (SWCNTs). Chitosan-wrapped carbon nanotubes are crosslinked to form a thin gel that is further functionalized with nitrilotriacetic acid (NTA) moieties. Upon chelation of Ni²+, the Ni²+ -NTA group binds to a hexa-histidine-modified troponin antibody, which specifically recognizes the target protein, troponin T. As the troponin T binds to the antibody, the local environment of the sensor changes, allowing for the detection through changes in SWCNT bandgap fluorescence intensity. In this work, we have developed the first near-infrared SWCNT sensor array for specific cTnT detection. Detection can be completed within 3 minutes, and the sensor responds linearly to the cTnT concentrations, with the experimental detection limit of 100 ng/ml (2.5 nM). This platform may provide a promising new tool for POC AMI detection in the future. Moreover, the work presented two useful methods of characterizing two commonly used functional groups, amines and carboxylic acids in soft gels, and this will be useful for other researchers studying hydrogel chemistry. In addition, we synthesized and characterized chitosan-gels both with and without NTA groups, and we compared fluorescence responses upon the addition of four different divalent cations, including Ni²+ , CO², Mg²+, and Mn²+. We proposed a model based Flory-Huggins theory, without any fitted parameters, that is able to describe the fluorescence increase as the Ni²+ concentration increases. The model suggests that the strong binding of Ni²+ onto NTA groups decreases the number of mobile ions in the gel, resulting in a reduction in the ionic chemical potential inside the gel. As a result, the gel de-swells, leading to a local SWCNT concentration increase and an increase in the SWCNT fluorescence signal. / by Jingqing Zhang. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996. / Includes bibliographical references (p. 119-130). / by Ann Park. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006. / Includes bibliographical references (p. 251-257). / Many technologically important processes in the chemical and mechanical industries involve coupled interactions of heat and mass transfer with chemical reactions - e.g. commercial burners, gas turbines, internal combustion engines, etc. However, detailed computational studies of such processes remain difficult at best, particularly due to the large reaction mechanisms that describe the chemical kinetics over the relevant range of reaction conditions. As a result, reduced models that contain fewer reactions and/or species while still capturing the "important" kinetics are often used in place of the full comprehensive reaction model in modeling complex reacting flows. "Adaptive Chemistry" - a method that uses several smaller locally-accurate reduced reaction models rather than a single "catch-all" model - has been shown in the combustion literature to be a viable option for improving computational efficiency in such studies. However, several outstanding challenges have prevented the adoption of this method in mainstream studies, most notably the difficulty of determining the accuracy of a solution obtained using Adaptive Chemistry. The focus of this research was to develop methods to enable efficient and accurate implementation of Adaptive Chemistry for reacting flow simulations. / (cont.) A method was developed for determining how much error may be tolerated in each reduced model in order to achieve a desired accuracy in Adaptive Chemistry solutions at steady-state. A novel model reduction method was also developed to obtain automatically reduced models (based on reaction elimination) that are guaranteed to satisfy the imposed error tolerances at all conditions in a user-specified range. In order to enable point-validated reduced models to be used accurately over ranges, an iterative method was developed for identifying ranges of reaction conditions over which such reduced models are guaranteed to remain valid. An Adaptive Chemistry method that demonstrates the application of these methods is presented. Efficient implementations of construction, storage and retrieval of reduced models that are appropriate for the reaction conditions encountered during Adaptive Chemistry simulations are presented, including an algorithm that adapts the library of reduced models to the solution trajectory "on the fly". / (cont.) The error-controlled Adaptive Chemistry method developed here is the first method that enables rigorous control of the model reduction error in steady-state Adaptive Chemistry solutions, as demonstrated in 1-D and 2-D premixed and partially premixed flame simulations. Results of a collaborative effort to facilitate engine research by developing the necessary cyberinfrastructure to provide remote access to the model reduction tools developed here are also discussed. Finally, methods are described for extending the error control criteria developed and demonstrated for reduced reaction models to reduced-species models and suggestions are made for future research in Adaptive Chemistry. / by Oluwayemisi Oluwi Oluwole. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1998. / Includes bibliographical references. / by Susan K. Hobbs. / Ph.D.