It was once thought either impossible or inefficient to photopolymerize a thickness greater than a thin film because of the optical attenuation of light into the depth of the sample. However, if several considerations are allowed, it is indeed possible. Three particular modifications are essential to enhance light penetration into the depth of the system. An initiator that absorbs in a region of the spectrum where no other components absorb maximizes the incident light intensity for photolysis of the initiator. Concentration and/or molar absorptivity of the initiator lower than typically used in thin films enhance light penetration. Finally, photobleaching initiators exhibit decreased absorbance upon photolysis and thus allow light to penetrate more deeply into the system with time. A need to model these systems is born out of the desirability to use light to initiate polymerizations of all sorts, including thicker systems. In this project, a set of differential equations describing the spatial and temporal evolution of the light intensity gradient, photoinitiator concentration gradient, and the photoinitiation rate profile are developed for a thick polymer system. The generalized model accounts for the consumption of initiator, evolution of the products of photolysis, diffusion of the initiator and photolysis products, and absorbance by all system components. The purpose of these studies was to characterize further these systems so that results accurately capture the photoinitiation process. Several key objectives have been accomplished, including the effects of illumination with polychromatic incident light, various illumination schemes, and verification of the predicative ability of the model. The ultimate goal of this project was two fold; first, to build a tool that models photopolymerization systems well, and second, to develop a means for choosing reaction components for photopolymerization applications. To understand and predict how these systems work contributes significantly to the photopolymerization field because it allows the user to predict system behavior accurately and to choose system components appropriate for a particular application.

The most prevalent polymerization methods are those which fall under the category of thermal polymerizations. The ease of initiation and the abundant knowledge present for these long time standards make implementation straightforward. However in some applications, the drawbacks may be numerous and the use of light induced polymerizations may be advantageous. Because of distinct advantages obtained using photopolymerizations as opposed to the more conventional thermally induced polymerizations science continues to further the knowledge and applications of photopolymers. Structured illumination is one such expansion of photopolymer knowledge and is a method by which variations in light intensity set up differential reaction rates evolving in the migration of monomer. The method can be tailored to produce cured systems with enhanced properties such as the reduction of stress or the control of gloss. Polymerization shrinkage is important for many applications since it leads to residual stresses which can deform a system and undermine its optical or mechanical properties. Also, while photopolymerized coatings are generally high in gloss, it is a characteristic of a polymer system that can have great impact on its function and appearance. Utilizing the simple method of structured illumination, and thereby controlling the coating system for both reductions of stress and gloss, can lead to great advantages for the finished product. This contribution looks at not only producing coatings using the method of structured illumination but also characterizes their properties by standard and unconventional means, alike. Mathematical modeling of the shrinkage, stress and monomer migration is also present in this work.

BiOWiSHTM – Aqua is a blend of preserved multi-bacteria culture with the capability of denitrification. If an anaerobic nitrate rich activation procedure is used instead of the standard aerobic activation procedure, the denitrification rate is increased by 28 percent under the conditions of 30°C, 1C:1N, 200mg/L of carbon, and 200mg/L nitrogen.

Photoelectrochemical cells have been intensively studied in recent years with regard to using thylakoid and photosynthesis system I/II. BBY membrane is another protein complex that has potential to be utilized to build photoelectrochemical cells. Within the BBY membrane lies the highly active photosynthesis system II complex, which upon light activation, generates electrons transported within the electron transport chain during photosynthesis in green plants. This study presents an approach of immobilizing thylakoid or BBY membrane onto gold nanoparticle modified gold plate or multi-walled carbon nanotube (MWCNT) modified indium tin oxide vi (ITO) coated glass substrate. The results show that BBY membrane has higher activity with a value of 168 ± 12 μmol DCIP/(mg Chl*hr) than the thylakoid, which has an activity of 67 ± 7 μmol DCIP/(mg Chl*hr). Further amperometric tests also show that BBY membrane generates a higher current than the thylakoid. We used gold based materials to build the cell first since gold has high electrical conductivity. However, in order to minimize the construction cost of cells, relatively cheap materials such as ITO coated glass and MWCNT were used instead. The surface morphology of cells was characterized using atomic force microscope (AFM) throughout cell modification. When comparing to the cell with gold material, the cell constructed with ITO and MWCNT generated a higher current density. The highest current density was found as 20.44 ± 1.58 μA/cm2 with a system of ITO/MWCNT/BBY. More, the stability of the system was examined and the result shows a decreasing rate of 0.78 %/hour.

Understanding the energetic and dynamic behavior of natural protein fluctuations is critical to elucidating important information associated with a multitude of protein functions including signaling processes, enzyme behavior, aggregation pathways etc... This information is also critically important in the development of novel and effective strategies aimed at target proteins associated with pathologies and disease. In order to obtain such useful information, tools and techniques are lacking that: 1) permit the efficient quantitative analysis of fluctuation behavior of existing protein structure ensembles and 2) permit computationally generated natural fluctuation states of proteins at relatively large timescales demanded by the need for biologically relevant results. This thesis presents such methods as well as the results of their application to a case study of Aβ40 and pathogenic Aβ42 where we identify key differences in energy interactions between those two isoforms. Additionally, our detailed atom-level analysis, was able to identify very minute differences in Ramachandran angles between the two strains as the cause for these interaction energy differences. We also demonstrate the efficacy of our implicit solvent algorithm in recovering independently, experimentally identified domain motion over a variety of protein systems. Such a system that is medically significant is the HIV-1 protease for which we identified significant motion of a flap domain known to be pharmaceutically important to the protease’s active site in drug targeting strategies. Lastly, we employ the insights thus acquired from the Aβ40/42 case study to see if Aβ42 aggregation inhibitors can be rationally developed and then tested in vitro for their efficacy. Results were very promising with Aβ42 aggregate sizes being significantly reduced by statistically significant margins by the inhibitor compounds. Due to these encouraging results, we have consequently obtained a provisional patent application for our inhibitors.

<p>Achieving control over the construction and operation of microfabricated label-free DNA biosensors would be a big leap in the quest for highly reliable clinical laboratory tests. Reliable outcomes of critical medical tests mean less need for repetitions and earlier isolation of outbreaks. Nanotechnology has lent itself well to this purpose, with a plethora of work that attempt to produce highly sensitive nano-biosensors for detection of DNA strands. The problem of achieving a repeatable outcome is crude at best. Additionally, the mechanism of sensing in label-free Field-Effect based DNA sensors is still a matter of dispute. Simulation of the sensors using physical models can shed light into these mechanisms and help answer this question. Computational calculations can also allow designers to assess the importance of several parameters involved in the fabrication.</p> <p>In this thesis, the problem of modeling FET-based DNA hybridization sensors (named BioFET) is approached. Using the Finite-Element Method, a scalable model for the BioFET is produced and solved in 3D. The results are compared to an earlier work and we find that higher dimension physical modeling is essential for more realistic results. Additionally, we present a model for the impedance of the BioFET which allows the calculation of parasitic components that can contaminate the impedance measurements.</p> <p>The issue of variations in the sensed signal from the BioFET is addressed by performing hybrid Finite-Element/Monte Carlo simulations on the conformation of single-stranded DNA. From electrostatic considerations alone, it is concluded that the change of conformation upon hybridization is a main contributor to the induced signal. We also simulate the positional variations of the DNA molecules on the sensitive surface. This computation yields an estimate for the amount of variation in the sensed signal due to the random placement of DNA molecules, and an estimate for the total signal-to-noise ratio is deduced.</p> / Doctor of Philosophy (PhD)

<p>While eye drops are a well-accepted and convenient method for ocular drug delivery, they exhibit significant limitations such as poor drug bioavailability, low ocular residence time, pulsatile delivery profiles in the tear fluid as well as the need for patient compliance. Silicone hydrogel (SH) contact lenses have been proposed as alternative ocular drug delivery systems due to their potential for targeted delivery to the corneal surface and high oxygen permeability. The ability of novel hyaluronic acid (HA)-containing silicone hydrogel materials to release timolol maleate (TM), an antiglaucoma drug, or ketotifen fumarate (KF), an anti-histamine administered for ocular allergies, was examined.</p> <p>The releasable wetting and the therapeutic agent were added to the pre-polymer mixture of the SH during synthesis through direct entrapment, while the reaction was performed by UV induced free-radical. The impact of the wetting agent on the swellability, surface wettability, optical transparency and <em>in vitro </em>drug release was studied.</p> <p>Simultaneous drug and wetting agent incorporation resulted in modified SH materials with slightly increased water content and significantly improved surface wettability. In addition, the optical transparency of these materials was not affected by drug loading. However, direct entrapment of HA decreased their optical clarity. <em>In vitro</em> release showed that TM was released over a 14 day period, whereas KF release lasted up to 36 days. For both therapeutic agents used in the current research, non-covalent entrapment of wetting agent and its MW did not significantly change the release kinetics, however the release rate of TM was slowed and controlled by the release of the HA, due to electrostatic interactions between the protonated TM and the anionic HA.</p> <p>The development of SH materials capable of simultaneously releasing a therapeutic and a wetting agent for an extended period of time and in a sustained manner can have a significant potential as extended drug delivery systems for the treatment of front of the eye diseases while also possibly providing comfort during wear.</p> / Master of Applied Science (MASc)

Oxidative stress is a pathophysiological condition defined by an increased production of reactive oxygen species (ROS), which can result in the growth arrest of cells followed by cell disintegration or necrosis. A number of small molecule antioxidants (e.g. curcumin, quercetin and resveratrol) are capable of directly scavenging ROS, thereby short-circuiting the self-propagating oxidative stress state. However, poor solubility and rapid 1st pass metabolism results in overall low bioavailability and acts as a barrier for its use as a drug to suppress oxidative stress efficiently. To overcome this limitation, these small molecule antioxidants were covalently conjugated into poly(β-amino ester) (PβAE) cross-linked networks to formulate prodrug gel microparticles and nanoparticles (nanogels). Being hydrolytically degradable in nature, these PβAE crosslinked systems released antioxidants in their original structural form in a sustained controlled fashion. Both quercetin and curcumin-PβAE nanogels showed prolonged suppression of cellular oxidative stress induced by H2O2. Curcumin PβAE nanogels also demonstrated protection against mitochondrial oxidative stress induced by H2O2 and polychlorinated biphenyls. Curcumin-PβAE gel microparticles were also developed as a platform to treat oral mucositis through a local antioxidant delivery route. The same synthesis chemistry was transferred to formulate resveratrol PβAE gel microparticles for topical applications, to treat UV radiation induced oxidative stress. Both formulations showed suppression of induced oxidative stress. An in vivo trial with curcumin-PβAE microparticles further showed relatively reduced the severity of induced oral mucositis (OM) in hamster check pouch as compared to placebo.

Despite recent advances in surgical technique and the development of numerous therapeutic agents, the formation post surgical adhesions (PSA) continues to cause complications for many patients. In this research, we have employed a rational system to develop a novel treatment to address this clinical need. Based on an understanding of the biochemical events that lead to PSA formation, a series of targeted polymeric biomaterials was designed to interrupt the fibrin gel matrix propagation and suppress PSA formation. Using group transfer polymerization, a series of well controlled block copolymers of polyacrylic acid and poly(ethylene glycol-methacrylate) based materials was synthesized. Subsequent functionalization with the pentapeptide Cys-Arg-Glu-Lys-Ala (CREKA) was employed to target the materials to fibrin as a marker of pro-adhesive sites. While preliminary testing of the untargeted materials verified their ability to suppress non-specific protein adsorption to model surfaces, numerous in vitro tests were conducted to study the ability to inhibit fibrin gel propagation. The ability to inhibit both the rate and quantity of fibrinogen deposition to a fibrin coated surface has been demonstrated. In addition, the rate of fibrin gel propagation and the degree of cellular attachment can modulated. Taking advantage of the systematic variation in structure facilitated by the robust synthetic methodology employed, statistical analysis was used to elucidate the structureproperty relationships governing the performance of these materials. The most important factors that lead to enhanced performance in in vitro tests are the length of PEG chain and number of peptide units conjugated to the polymer: increasing PEG chain length and increasing the number of peptides conjugated to the polymer both improve performance in all tests. The synthetic methods that have been developed, in conjunction with the experimental results, will be used to direct future studies, including cytotoxicity and animal studies.

The chemical diversity and biological activities of terpene and terpenoids have served in the development of new flavors, fragrances, medicines and pesticides. While terpenes are made predominantly by plants and microbes in small amounts and as components of complex mixtures, chemical synthesis of terpenes remains technically challenging, costly and inefficient. In this dissertation, methods to create new yeast lines possessing a dispensable mevalonate biosynthetic pathway wherein carbon flux can be diverted to build any chemical class of terpene product are described. The ability of this line to generate diterpenes was next investigated. Using a 5.5 L fed bath fermentation system, about 569 mg/L kaurene and approximately 207 mg/L abietadiene plus 136 mg/L additional isomers were achieved. To engineer more highly modified diterpenes might have greater industrial, agricultural or medicinal applications, kaurenoic acid production reached 514 mg/L with byproduct kaurene and kaurenal at 71.7mg/L and 20.1mg/L, respectively, in fed batch fermentation conditions. Furthermore, ZXM lines for engineer monoterpene and ZXB lines for engineer triterpene were generated by additional specific genomic modification, 84.76 ±13.2 mg/L linalool, 20.54±3.8 mg/L nerolidol and 297.7mg/L squalene were accumulate in ZXM144 line ana ZXB line, respectively, in shake flask conditions.