Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2009. / Includes bibliographical references (p. 141-151). / Utilization of nanoparticle heating for controlled release application was proposed and its feasibility was explored. The proposed method was formulated by realizing that biomolecule - nanoparticle conjugation is heat sensitive and both their dimensions are in the same length scale. This exploration centered on showing the proof of concept that conjugated biomolecules can be released from the nanoparticle surface in a controlled manner by heating the nanoparticles via external energy sources. The selectivity of the multiple releases was also investigated. Two mechanisms of nanoparticle heating were explored. The AC magnetic heating of magnetic nanoparticles has limitation due to its low-power energy delivered to nanoparticles. The irradiation of femtosecond laser pulses on the absorbing gold nanorods provides the answer to this limitation due to the very high-power of energy delivery through these ultrashort pulses. We developed gold nanorod surface customization technique to enable DNA - nanorod conjugation, thus turning gold nanorods into nanoscale carriers. Pulsed laser excitation in resonance with their absorption peaks can heat and melt the nanorods. This is exploitable for controlling the release of DNA oligonucleotides conjugated onto the nanorod surface. Nanorods with different aspect ratios absorb light at different wavelengths and thus can be excited independently. We have successfully demonstrated the selective releases of two distinct DNA oligonucleotides, where each is released from a different type of nanorod. / This was accomplished by the laser excitation at two different wavelengths corresponding to both of the nanorods' absorption peaks. The releases were very selective, efficient, and externally tunable by adjusting the laser fluence. The released DNA oligos were still functional. This concept is expandable to beyond two species. Its thiol conjugation chemistry is versatile and capable of high loading. With these advantageous factors, this proof of concept of selective multiple triggered releases from gold nanorods have a great potential as a new strategy for multiple controlled released application. / by Andy Wijaya. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Colloidal dispersion of nanoparticles (CNPs) has interesting properties both in terms of fundamental studies and industrials applications. Particular focus on the phase equilibrium and separation dynamics of CNPs has been necessary for understanding how exactly and fast CNPs are assembled and for controlling the assembly structure and dynamic properties. For understanding and controlling assembly structure and dynamics of CNPs, theoretical analysis in conjunction with computational approaches supported by experimental validation is necessary. In this thesis, studies on the phase-equilibrium-mediated assembly of CNPs are performed by using various computational tools accompanied by theoretical modeling to cover wide range of spatio and temporal dimensions of the desired system containing CNPs. To address the phase separation of CNPs, we studied on two main mechanisms; (1) cluster formation and (2) spinodal decomposition. In each mechanism, we developed novel, effective, and efficient computational algorithms to elucidate phase-equilibrium assembly structure and formation dynamics of CNPs: (1) a kinetic Monte Carlo (KMC) algorithm for cluster formation in microscopic dimensions and spinodal decomposition of homogeneous mixture of CNPs in mesoscopic scale, (2) a self-consistent mean-field (SCMF) model for surface-directed separation of a binary mixture of CNPs in mesoscopic-macroscopic scale, and (3) the spectral method for spinodal decomposition of a binary or ternary mixture of CNPs in macroscopic scale. All the algorithms and results from the simulations were verified by either mathematical proofs or comparisons to other computational methods. In particular, proof-of-concept experimental results of the fabricition of a functional thin film in which a binary mixture of CNPs form the controlled gradient concentrations profile across the thickness direction were presented. On the basis of the experimental demonstration, we showed the validity of the computational model and possible future applications of the fabricated thin film as an optically-functional material. The computational algorithms and numerical tools developed in this thesis supported by theoretical analysis and experimental demonstration can be applicable to various dynamic problems regarding CNPs, especially, for the complicated cases including multi-component, multi-phase systems. We expect that the work performed in this thesis can provide a substantial advantage for future research, such as controlled cluster formation of CNPs by polymer gel mesh, cluster formation of Janus CNPs, and physically controlled spinodal decomposition of CNPs in thin films, as well as progressive application to preparation of novel devices. / by Seok Joon Kwon. / Ph. D.

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1939. / MIT copy bound with: Regenerator performance / R. W. Arns, F. N. Bent, P. W. Comstock, J. A. Lucas. 1939. / Includes bibliographical references (leaf 29). / by Norman G. Farquhar, Henry R. Landwehr. / B.S.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 129-134). / Diagnostic tests in resource-limited settings require technologies that are affordable and easy-to-use with minimal infrastructure. Colorimetric detection methods that provide results that are readable by eye, without reliance on specialized and expensive equipment, have great utility in these settings. Existing colorimetric methods based on enzymatic reactions and gold nanoparticles often produce results that must be read within a specified time interval to ensure their validity. In many instances, a user has to wait several minutes for the color to develop. Moreover, the result can be interpreted incorrectly because of low visual contrast. Therefore, a colorimetric detection technology that produces bright and unambiguous readout within a time interval of a few seconds to less than two minutes, and removes the burden of accurate time keeping from the user can be very beneficial in low-resource settings. Photo-initiated polymerization-based amplification (PBA) is a technology that allows detection of a surface-bound analyte through co-localization of a visible-light photoinitiator with the analyte present on the surface. In the presence of an appropriate dose of light and monomers, a subsequent free radical polymerization reaction results in formation of an interfacial hydrogel in areas where the initiator has been localized. In this thesis, we modified the eosin/tertiary amine-based PBA technology, which had previously been developed on transparent glass surfaces, for use with cellulose-based (paper) surfaces. Using Plasmodium falciparum histidine-rich protein as an example, we showed that paper-based PBA allowed high-contrast visual detection of proteins with a limit-of-detection of single digit nM concentration (~7 nM) in complex matrices such as human serum and plasma purified from blood samples through the use of a hand-operated microfluidic device. The paper-based immunoassay required only 10 [mu]L sample per test and the total time for signal amplification, from illumination to colorimetric detection, was 2-2.5 minutes per test. The method provided quantitative information regarding analyte levels when combined with cellphone-based imaging. It also allowed decoupling of the capture of analyte on the surface from the signal amplification and visualization steps. We showed that in comparison with enzymatic amplification methods and silver deposition on gold nanoparticles, PBA-based readout on paper was cheaper, easier to perceive at its limit-of-detection, and had the lowest incidence of false readouts due to timing errors. In addition to developing PBA for use in paper devices, we combined PBA with a dilution array approach for quantifying analyte levels by counting number of visible polymer spots on a biochip. We used an empirical design approach that did not depend on measurement of equilibrium and kinetic binding parameters of the antibodies used in the assay and provided a dynamic range of three orders of magnitude, 70 pM to 70 nM, for visual quantification of the analyte. We also built a portable, light-weight, and customizable LED-based device with automated timer functionality for use with PBA assays in point-of-care settings. / by Shefali Lathwal. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 106-116). / Microorganisms are promising hosts for the production of valuable chemicals, such as polymer and pharmaceutical precursors, fuel alternatives, flavors and fragrances. Achieving high yields of a product is often restricted by the interconnectivity of pathways in cells and finite nature of cellular resources. To overcome these limitations, dynamic pathway regulation has emerged as a strategy to balance flux between growth and production, such that titers and yields are maximized. Here, we demonstrate that dynamic pathway regulation by down-regulating competing enzymes can successfully improve yields of products. In Saccharomyces cerevisiae, we constructed a hexokinase valve where Hxk2 and GIk1 were deleted and the only remaining Hxk1 was placed under control of the tetracycline transactivating system (tTA) that enables repression of Hxk1 up to 10-fold in activity upon addition of doxycycline. Downregulation of this competing Hxk1 enzyme resulted in a 50-fold increase in gluconic acid and a 3-fold improvement in isobutanol yields from glucose. Extending this concept to other microorganisms, engineering downregulation of competing enzymes is dependent upon the ability to deplete a protein of interest in an inducible manner in the production host. In Pseudomonas spp., tools for specific protein depletion remain limited. Current methods involve promoter replacements and addition of degradation tags that require editing the genome, a process that can be laborious in Pseudomonas. Here, we developed a CRISPRi gene repression system by engineering the Streptococcus pasteurianus dCas9 and sgRNA. We demonstrate a robust and titratable gene depletion system, with up to 100-fold repression in [beta]-galactosidase activity in P. aeruginosa. We performed the first in vivo characterization of PAM site preferences of S. pasteurianus dCas9, revealing that targeting both NNGTGA and NNGCGA within the promoter can provide robust repression. Finally, the developed CRISPRi gene depletion system enabled the downregulation of competing muconate cycloisomerase in P. putida, leading to accumulation of muconic acid. In summary, we show that dynamic regulation of pathways by downregulating competing enzymes is an effective method to improve titers and yields of products. Controlling enzyme abundance at the transcriptional level proved successful with the existing tTA system in S. cerevisiae and with our developed CRISPRi system in Pseudomonas. / by Sue Zanne Tan. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1991. / Includes bibliographical references (leaves 252-259). / by Susan Lew. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1993. / Includes bibliographical references (v. 2, leaves 356-366). / by Jospeh Allen Marr. / Ph.D.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996. / Includes bibliographical references (leaves 218-229). / by Ranganathan S. Godavarti. / Sc.D.

Massachusetts Institute of Technology. Dept. of Chemical Engineering. Thesis. 1966. Sc.D. / Bibliography: p. 311-320. / Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005. / In title on t.p., "beta" appears as lower-case Greek letter. / Includes bibliographical references. / Genetic vaccination is the administration of nucleic acids to induce cellular expression of antigens, leading to an immune response. Unlike traditional vaccines, this technology has tremendous potential for treating or preventing diseases such as HIV, malaria, and cancer. However, this potential is currently unrealized because of the safety concerns which plague viral vaccine carriers and the inefficiency of nonviral delivery systems when compared to their viral counterparts. A promising and versatile nonviral delivery method for genetic vaccines involves microencapsulation of antigen-encoding DNA, because such particles protect their payload and target it to phagocytic, antigen-presenting immune cells. However, the biomaterial conventionally used in these microparticle formulations, an FDA-approved polyester called poly lactic-co-glycolic acid (PLGA), was not designed specifically to deliver DNA, takes too long to release encapsulated payload, and therefore fails to induce high levels of target gene expression. A new class of novel biomaterials have been synthesized called poly([beta]-amino ester)s which are biodegradable and can have similar physical properties to PLGA, but are pH-sensitive and have gene delivery functionalities. / (cont.) Using these materials we can fabricate microparticle-based delivery systems which have relatively high DNA loadings and can significantly buffer the destructive acidic pH microenvironment created by ester bond degradation. These formulations generate an increase of up to 5 orders of magnitude in DNA delivery efficiency when compared to PLGA alone and can be potent stimulators of antigen presenting cells in vitro. We have also demonstrated that incorporating these new biomaterials into microparticulate genetic vaccines can lead to antigen-specific, immune-mediated rejection of a lethal tumor dosage in vivo, a significant advance over conventional formulations. Finally, with the synthesis of libraries containing thousands of structurally diverse PBAEs, it is warranted to develop new methods of fabrication which enable the high-throughput screening of such libraries. Herein, we describe, for the first time, such a rapid fabrication technique and demonstrate that plasmid encapsulated in these formulations is transcriptionally active. / by Steven Little. / Ph.D.