Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1939. / Includes bibliographical references (leaves 58-60). / by Charles R. Houssiere, Jr. / M.S.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1995. / Includes bibliographical references (leaves 140-141). / by Scott W. Borland. / M.S.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2000. / Includes bibliographical references. / Polycyclic aromatic hydrocarbons (P AH) and soot are formed when a hydrocarbon fuel is oxidized under fuel-rich conditions. The distinction between what constitutes the largest P AH molecule and the smallest soot particle is arbitrary; the formation processes of both can be placed under the heading of molecular weight growth. Evidence exists for the carcinogenicity of many P AH molecules. Soot is used as a component of dyes and as an additive to rubbers as well as being an undesirable atmospheric pollutant. Both are emitted from many typical combustion processes such as diesel engines, wood fires, furnaces, etc. Though the area has received much attention, the fundamental chemical mechanisms for formation of both P AH and soot are still uncertain. Much debate has centered on the identity of the soot surface growth reactant, in particular whether the dominant surface growth reactant is P AH or acetylene. Though several models of soot formation exist, none has demonstrated through comparison to experimental data a thorough knowledge of the fundamental chemical processes of soot formation. The goal of this research was to further the understanding of these fundamental chemical processes. Since the chemistry of P AH and soot are intertwined, PAH was a necessary subcomponent of the soot formation research. The research was accomplished by obtaining soot particle size distribution data for the jet-stirred reactor/ plug-flow reactor (JSR/PFR), development of kinetics modeling methods, and the development of a kinetics model of soot formation. The JSR/PFR has been used extensively in the past to investigate P AH and soot formation, providing much data for concentrations of light-gas species, P AH, and soot under various conditions of equivalence ratio, temperature, and PFR additives. No experimental data have been obtained for soot particle size distribution in the JSR/PFR, so a study was undertaken here to obtain the soot particle size distributions for two conditions previously studied by Marr, premixed atmospheric ethylene combustion at equivalence ratio 2.2 and temperatures of 1520 K and 1620 K. Thermophoretic sampling was used to obtain soot samples for transmission electron micrograph analysis. Software was written and used to obtain soot particle sizes from electron micrographs. The chemical environment in a fuel-rich flame consists of many hundreds of species and thousands of chemical reactions. To isolate particular portions of the chemistry, a calculational technique was developed, data incorporation, that replaces chosen portions of the chemistry in kinetics models with functions of data concentrations. This technique was then used to isolate the process of P AH molecular weight growth and soot nucleation through the use of a discrete sectional model, and rate coefficients for hydrogen-atom abstraction, acetylene-addition, and PAH radical addition to PAH were obtained by comparisons to data from Marr for the 1620 K condition described above and the same condition with naphthalene injection into the PFR. The data incorporation technique was then used to expand the discrete sectional model to include sections describing soot, and the experimental soot size distribution data described above was used with previously available PFR data to obtain values for rate coefficients of PAHaddition to soot and coagulation of soot particles. Five PFR conditions were used to develop the soot formation model in these calculations, and the dominant mechanisms of soot formation present under these conditions appear to be present in the model. Quantitative agreement is obtained to all of the available data, including simultaneous agreement of soot mass and particle size, without significant deviation in the rate coefficients required to obtain agreement. Calculations were performed using both PAH and acetylene as the dominant soot surface growth reactant. It was found that P AH had far more consistent rate coefficient values (constant to within a factor of 4) than acetylene ( constant to within a factor of 59) to describe the data for all of the conditions. An analysis of the above five sets of conditions in the PFR, an additional three for the PFR, and three for premixed one-dimensional flames of acetylene, ethylene, and benzene, for which concentrations of acetylene, P AH. and soot, and in the case of the one-dimensional flames, soot particle size data, were available, were analyzed with the aim of understanding the dominant characteristics of the soot surface growth reactant. Soot mass growth rates were calculated for all of the conditions, and deviate markedly between the PFR and one-dimensional flames. Soot growth rate increases and oscillates in the PFR and sharply declines in the one-dimensional flames in the region of soot growth after initial particle inception. Under all of these conditions, PAH show the characteristics required of the dominant surface growth reactant: increases and oscillations in the PFR and sharp declines in the one-dimensional flames. For acetylene to be the dominant surface growth reactant, anomalous behavior of acetylene-suot reactivity would be required that cannot be explained by soot aging or radical intermediates. This leads to the observation that the long-held notion of declining soot reactivity in premixed one-dimensional flames similar to the ones studied here is a result of variations in the PAH intermediates and not a real phenomenon in the region after soot particle inception. An approximate method of uncertainty analysis of kinetics models was used to place an uncertainty bound of a factor of 3 on the rate coefficient parameters calculated. The approximate method was compared to more precise techniques and used to show that the uncertainty of concentration predictions with PAH kinetics models is of very large magnitude. The approximate uncertainty analysis technique was also used to show that the data incorporation technique reduces the uncertainty in calculated rate parameters by over two orders of magnitude. A kinetics model reduction algorithm was developed and implemented to reduce a PAH kinetics model fro.n 722 reactions and 187 species to 93 reactions and 52 species, maintaining naphthalene conc1;;ntration to within 9% of the original model. This technique was also used by Dinaro to redm:e a benzene oxidation model from 545 to 41 reactions for use in super-critical water oxidation applications. / by David Franklin Kronholm. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008. / Includes bibliographical references (p. [135]-143). / The ability to visually observe single DNA molecules has greatly improved our understanding of polymer physics, from gel electrophoresis to the theology of dilute (and even concentrated) polymer solutions. The use of DNA in these general studies, though, resulted in a depth of specific knowledge concerning a particular polymer of major interest in biology. Researchers have taken advantage of this wealth of knowledge to develop new, faster, cheaper, and more direct methods of extracting the information, at a coarse level, embedded in the sequence of basepairs along the DNA backbone. Further development, though, is now limited by the ability to control and manipulate the position and conformation of single DNA molecules. It was recognized long ago that confinement of polymer molecules in geometries with dimensions on the order of the polymer size would greatly affect the physical behavior of that polymer. These physical changes were later hypothesized to be of use to control single molecules of DNA. However, until recently, the confinement theories and their use stood untested due to a lack of techniques to reliably and controllably construct micro- (and nano-) devices with such small feature sizes. It is the focus of this thesis to investigate these confinement effects in an ideal, nanofabricated geometry and their use in the manipulation and control of single DNA molecules. In this thesis, we present a series of single-molecule visualization studies aimed at elucidating polymer behavior in confinement and methods of possible use in the manipulation and control of the polymer conformation. In particular, confinement in a slit was shown, both experimentally and through scaling analysis, to diminish long length scale polymer-induced solvent flow sufficiently enough to render those effects negligible in the behavior of the confined molecule. We also demonstrate that confinement also alters the diffusion and relaxation time of the DNA, and we compare their dependence on channel height and molecular weight to existing theories. / (cont.) De Gennes' blob theory is found to describe the molecular weight scalings quite well, but predictions of the scalings with channel height are plagued by an oversimplified description of short length scale polymer-solvent interaction used in the theory. Thus, empirical knowledge is needed to adequately predict the scaling of DNA transport coefficients in confinement. We also investigate aspects of polymer deformation in confinement. We observe, for the first time, two slow modes of polymer relaxation. The two modes are found to govern polymer behavior based on the polymer's extension, a phenomenon unique to confinement in polymer physics. A simple, physical model is developed to explain the origin of the two governing time scales, to explain their scaling with channel height and molecular weight, and to predict the extension at which the exchange between the two timescales occurs. We also examine the effects of these two characteristic time constants on the steady-state stretch of molecules in confinement. We find that the second-longest relaxation time determines the deformation rate needed to unravel the coil, unlike bulk polymer deformation. Interestingly, details of this unraveling change significantly in confinement, highlighting the need for further work in this area. In larger channels, we demonstrate that microfabrication techniques in the form of an obstacle array with dimensions smaller than the polymer size can aid polymer stretching. While a polymer will often fold or kink during stretching, we find the use of a collision event to "precondition" the polymer conformation for stretching makes these folds and kinks less likely, and therefore, stretching occur more rapidly. The efficiency of the device depends strongly on the probability of a collision event, and results from single molecule/single post experiments are used to demonstrate the capability of a second-generation device. The impact of this thesis will be two-fold. Our fundamental results have and will continue to serve as a basis of comparison and a springboard for more complicated studies of confined polymer physics. / (cont.) These studies provide detailed information on DNA transport coefficients in geometries widely utilized in microfabricated devices. We also directly display the effects of confinement on DNA manipulation. Non-equilibrium polymer dynamics are found to be highly nontrivial, exemplified by the importance of a new timescale of polymer motion. Importantly, it is this new timescale that is of concern for applications such as gene mapping where large scale polymer deformation is required. Lastly, we demonstrate the success of a unit-operation-like approach to the design of polymer manipulation devices. / by Anthony Balducci. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1995. / Includes bibliographical references. / by Árpád Bence Palotás. / M.S.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1962. / Vita. / Includes bibliographical references (leaves 229-234). / by Adel F. Sarofim. / Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1998. / Includes bibliographical references (p. 241-246). / by David C. Oda. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 259-274). / This thesis addresses the challenges brought forth by the shale oil and gas revolution through the application of formal optimization techniques. Two frameworks, each addressing the monetization of shale oil and gas resources at different ends of the scale spectrum, are developed. Importantly, these frameworks accounted for both the dynamic and stochastic aspects of the problem at hand. The first framework involves the development of a strategy to allocate small-scale mobile plants to monetize associated or stranded gas. The framework is applied to a case study in the Bakken shale play where large quantities of associated gas are flared. Optimal strategies involving the continuous redeployment of plants are analyzed in detail. The value of the stochastic solution with regards to uncertainty in resource availability is determined and it indicates that mobile plants possess a high degree of flexibility to handle uncertainty. The second framework is a comprehensive supply chain optimization model to determine optimal shale oil and gas infrastructure investments in the United States. Assuming two different scenario sets over a time horizon of twenty-five years, the features of the optimal infrastructure investments and associated operating decisions are determined. The importance of incorporating uncertainty into the framework is demonstrated and the relationship between the stability of the stochastic solution and the variance of the distribution of future parameters is analyzed. The thesis also analyzes the Continuous Flow Stirred Tank Reactor (CFSTR) equivalence principle as a method for screening and targeting favorable reaction pathways, with applications directed towards gas-to-liquids conversion. The principle is found to have limited usefulness when applied to series reactions due to an unphysical independence of the variables which allows for the maximization of production of any intermediate species regardless of the magnitude of its rate of depletion. A reformulation which eliminates the unphysical independence is proposed. However, the issue of arbitrary truncation of downstream reactions remains. / by Siah Hong Tan. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2007. / Includes bibliographical references. / Molecular self-assembly describes the assembly of molecular components into complex, supramolecular structures governed by weak, non-covalent interactions. In recent years, molecular self-assembly has been used extensively as a means of creating materials and devices with well-controlled, nanometer-scale architectural features. In this thesis, molecular self-assembly is used as a tool for the fabrication of both gene and drug delivery systems which, by virtue of their well-controlled architectural features, possess advantageous properties relative to traditional materials used in these applications. The first part of this thesis describes the solution-phase self-assembly of a new family of linear-dendritic "hybrid" polymers with plasmid DNA for applications in gene therapy. It begins with an overview of the design of next-generation, non-viral gene delivery systems and continues through the synthesis and validation of hybrid polymer systems, which possess modular functionalities for DNA binding, endosomal escape, steric stabilization, and tissue targeting. This part of the thesis concludes with applications of these systems to two areas of clinical interest: DNA vaccination and tumor targeted gene therapy. / (cont.) The second part of this thesis describes the directed self-assembly of polymeric thin films which are capable of degrading in response to either passive or active stimuli to release their contents. It begins with a description of passive release thin films which degrade by basic hydrolysis to release precise quantities of model drug compounds. These systems can be engineered to release their contents on time scales ranging from hours to weeks and can also be designed to release multiple drugs either in series or in parallel. Later, field-activated thin films which release their contents in response to an external, electrical stimulus are described and characterized in detail. Together, these approaches combine rapid and inexpensive processing, the ability to conformally coat any surface regardless of composition, size, or shape, and the ability to release multi-drug or multi-dose schedules, and as such they may find applications in a range of areas. / by Kris Cameron Wood. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Repetitive DNA sequences are prevalent in both prokaryote and eukaryote genomes and the majority of repeats are concentrated in intergenic regions. These tandem repeats (TRs) are highly variable as the number of repeated units changes frequently due to recombination events and/or polymerase slippage during replication. While TRs have been traditionally regarded as non-functional 'junk' DNA, variability in the number of TRs present within or close to genes is known to lead to gross phenotypic changes and disease. However, whether intergenic TRs have a functional role is less understood. Recent studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if repeated binding sites serve as decoys, and alter the expression of genes regulated by the sequestered TF. Combining experiments with kinetic modeling suggests that repeated decoy binding sites sequester activators more strongly than a promoter binding site although both binding sites are identical in sequence. This strong binding converts a graded dose-response between activator and promoter to a sigmoidal-like response. We further find that the tight activatordecoy interaction becomes weaker with increasing activator levels, suggesting that the activator binding at the repeated decoy site array might be anti-cooperative. Finally, we show that the high affinity of repeated decoy sites qualitatively changes the behavior of a transcriptional positive feedback loop from a graded to bimodal, all-or-none response. Taken together, repeated TF binding sites play an unappreciated role as a gene regulator. Since repeated decoy sites are hypervariable in number, this variability can lead to qualitative changes in gene expression and potentially phenotypic variation over short evolutionary time scales. / by Tek Hyung Lee. / Ph.D.