Group- III nitride based semiconductors have emerged as the leading material for short wavelength optoelectronic devices. The InGaN alloy system forms a continuous and direct bandgap semiconductor spanning ultraviolet (UV) to blue/green wavelengths. An ideal and highly efficient light-emitting device can be designed by enhancing the spontaneous emission rate. This thesis deals with the design and fabrication of a visible light-emitting device using GaN/InGaN single quantum well (SQW) system with enhanced spontaneous emission. To increase the emission efficiency, layers of different metals, usually noble metals like silver, gold and aluminum are deposited on GaN/InGaN SQWs using metal evaporator. Surface characterization of metal-coated GaN/InGaN SQW samples was carried out using atomic force microscopy (AFM) and scanning electron microscopy (SEM). Photoluminescence is used as a tool for optical characterization to study the enhancement in the light emitting structures. This thesis also compares characteristics of different metals on GaN/InGaN SQW system thus allowing selection of the most appropriate material for a particular application. It was found out that photons from the light emitter couple more to the surface plasmons if the bandgap of former is close to the surface plasmon resonant energy of particular metal. Absorption of light due to gold reduces the effective mean path of light emitted from the light emitter and hence quenches the quantum well emission peak compared to the uncoated sample.

Surface Plasmon Resonance (SPR) and localized surface plasmon resonance (LSPR) biosensors have brought a revolutionary change to in vitro study of biological and biochemical processes due to its ability to measure extremely small changes in surface refractive index (RI), binding equilibrium and kinetics. Strategies based on LSPR have been employed to enhance the sensitivity for a variety of applications, such as diagnosis of diseases, environmental analysis, food safety, and chemical threat detection. In LSPR spectroscopy, absorption and scattering of light are greatly enhanced at frequencies that excite the LSPR, resulting in a characteristic extinction spectrum that depends on the RI of the surrounding medium. Compositional and conformational change within the surrounding medium near the sensing surface could therefore be detected as shifts in the extinction spectrum. This dissertation specifically focuses on the development and evaluation of highly sensitive LSPR biosensors for in situ study of biomolecular binding process by incorporating nanotechnology. Compared to traditional methods for biomolecular binding studies, LSPR-based biosensors offer real-time, label free detection. First, we modified the gold sensing surface of LSPR-based biosensors using nanomaterials such as gold nanoparticles (AuNPs) and polymer to enhance surface absorption and sensitivity. The performance of this type of biosensors was evaluated on the application of small heavy metal molecule binding affinity study. This biosensor exhibited ~7 fold sensitivity enhancement and binding kinetics measurement capability comparing to traditional biosensors. Second, a miniaturized cell culture system was integrated into the LSPR-based biosensor system for the purpose of real-time biomarker signaling pathway studies and drug efficacy studies with living cells. To the best of our knowledge, this is the first LSPR-based sensing platform with the capability of living cell studies. We demonstrated the living cell measurement ability by studying the VEGF signaling pathway in living SKOV-3 cells. Results have shown that the VEGF secretion level from SKOV-3 cells is 0.0137 ± 0.0012 pg per cell. Moreover, we have demonstrated bevacizumab drug regulation to the VEGF signaling pathway using this biosensor. This sensing platform could potentially help studying biomolecular binding kinetics which elucidates the underlying mechanisms of biotransportation and drug delivery.

Glucans are cell wall constituents of fungi and bacteria that bind to pattern recognition receptors and modulate innate immunity, in part, by macrophage activation. We used surface plasmon resonance to examine the binding of glucans, differing in fine structure and charge density, to scavenger receptors on membranes isolated from human monocyte U937 cells. Experiments were performed at 25°C using a biosensor surface with immobilized acetylated low density lipoprotein (AcLDL). Inhibition of the binding by polyinosinic acid, but not polycytidylic acid, confirmed the interaction of scavenger receptors. Competition studies showed that there are at least two AcLDL binding sites on human U937 cells. Glucan phosphate interacts with all sites, and the CM-glucans and laminarin interact with a subset of sites. Polymer charge has a dramatic effect on the affinity of glucans with macrophage scavenger receptors. However, it is also clear that human monocyte scavenger receptors recognize the basic glucan structure independent of charge.

No description available.

The current thrust towards developing silicon compatible integrated nanophotonic devices is driven by need to overcome critical challenges in electronic circuit technology related to information bandwidth and thermal management. Surface plasmon nanophotonics represents a hybrid technology at the interface of optics and electronics that could address several of the existing challenges. Surface plasmons are electronic charge density waves that can occur at a metal-dielectric interface at optical and infrared frequencies. Numerous plasmon based integrated optical devices such as waveguides, splitters, resonators and multimode interference devices have been developed, however no standard integrated device for coupling light into nanoscale optical circuits exists. In this thesis we experimentally and theoretically investigate the excitation of propagating surface plasmons via resonant metal nanoparticle arrays placed in close proximity to a metal surface. It is shown that this approach can lead to compact plasmon excitation devices. Full-field electromagnetic simulations of the optical illumination of metal nanoparticle arrays near a metal film reveal the presence of individual nanoparticle resonances and collective grating-like resonances related to propagating surface plasmons within the periodic array structure. Strong near-field coupling between the nanoparticle and grating resonances is observed, and is successfully described by a coupled oscillator model. Numerical simulations of the effect of nanoparticle size and shape on the excitation and dissipation of surface plasmons reveal that the optimum particle volume for efficient surface plasmon excitation depends sensitively on the particle shape. This observation is quantitatively explained in terms of the shape-dependent optical cross-section of the nanoparticles. iv Reflection measurements on nanoparticle arrays fabricated using electron-beam lithography confirm the predicted particle-grating interaction. An unexpected polarizationdependent splitting of the film-mediated collective resonance is successfully attributed to the existence of out-of plane polarization modes of the metal nanoparticles. In order to distinguish between the excitation of propagating surface plasmons and localized nanoparticle plasmons, spectrally resolved leakage radiation measurements are presented. Based on these measurements, a universally applicable method for measuring the wavelength dependent efficiency of coupling free-space radiation into guided surface plasmon modes on thin films is developed. Finally, it is shown that the resonantly enhanced near-field coupling the nanoparticles and the propagating surface plasmons can lead to optimized coupler device dimensions well below 10 m.

Cholera toxin (CT), secreted from Vibrio cholerae, causes a massive fluid and electrolyte efflux in the small intestine that results in life-threatening diarrhea and dehydration which impacts 3-5 million people per year. CT is secreted into the intestinal lumen but acts within the cytosol of intestinal epithelial cells. CT is an AB5 toxin that has a catalytic A1 subunit and a cell binding B subunit. CT moves from the cell surface to the endoplasmic reticulum (ER) by retrograde transport. Much of the toxin is transported to the lysosomes for degradation, but a secondary pool of toxin is diverted to the Golgi apparatus and then to the ER. Here the A1 subunit detaches from the rest of the toxin and enters the cytosol. The disordered conformation of free CTA1 facilitates toxin export to the cytosol by activating a quality control mechanism known as ER-associated degradation. The return to a folded structure in the cytosol allows CTA1 to attain an active conformation for modification of its Gsα target through ADP-ribosylation. This modification locks the protein in an active state which stimulates adenylate cyclase and leads to elevated levels of cAMP. A chloride channel located in the apical enterocyte membrane opens in response to signaling events induced by these elevated cAMP levels. The osmotic movement of water into the intestinal lumen that results from the chloride efflux produces the characteristic profuse watery diarrhea that is seen in intoxicated individuals. The current model of intoxication proposes only one molecule of cytosolic toxin is required to affect host cells, making therapeutic treatment nearly impossible. However, based on emerging evidence, we hypothesize a threshold quantity of toxin must be present within the cytosol of the target cell in order to elicit a cytopathic effect. Using the method of surface plasmon resonance along with toxicity assays, I have, for the first time, directly measured the efficiency of toxin delivery to the cytosol and correlated the levels of cytosolic toxin to toxin iv activity. I have shown CTA1 delivery from the cell surface to the cytosol is an inefficient process with only 2.3 % of the surface bound CTA1 appearing in the cytosol after 2 hours of intoxication. I have also determined and a cytosolic quantity of more than approximately .05ng of cytosolic CTA1 must be reached in order to elicit a cytopathic effect. Furthermore, CTA1 must be continually delivered from the cell surface to the cytosol in order to overcome the constant proteasome-mediated clearance of cytosolic toxin. When toxin delivery to the cytosol was blocked, this allowed the host cell to de-activate Gs, lower cAMP levels, and recover from intoxication. Our work thus indicates it is possible to treat cholera even after the onset of disease. These findings challenge the idea of irreversible cellular toxicity and open the possibility of postintoxication treatment options.

The glycoprotein CD36 is expressed in the plasma membrane (PM) of many cell types that surround or contact arteries, including macrophages, myocytes, and endothelial cells. CD36 binds oxidized low density lipoprotein (oxLDL), which promotes atherosclerosis, and fatty acids (FA), which promotes their cellular uptake. To gain insights into the molecular mechanisms of uptake, HEK293 cells expressing CD36 were studied by cell biological and fluorescence methods. To test our hypothesis that the PM is not an impermeable barrier to FA and that FA move into cells by diffusion via their uncharged form, we first applied biophysical fluorescence spectroscopy to directly measure transmembrane FA movement and membrane fluidity. Expression of CD36 in HEK293 cells did not increase either transport across the PM or the fluidity of the PM compared to HEK293 cells without CD36; however, CD36 enhanced intracellular FA esterification. Furthermore, the widely used “inhibitors” of FA transport did not alter either the rapid FA transmembrane diffusion in HEK293 cells or diffusion in control experiments with protein-free phospholipid bilayers. To gain new insights into the physiological relevance of FA binding to CD36, we applied surface plasmon resonance (SPR) to quantify FA and oxLDL binding to the ectodomain of CD36. Structurally distinct FA [saturated, monounsaturated (cis and trans), polyunsaturated, ω-3, ω-6, and oxidized FA] were pulsed in a solubilized form (bound to methyl-β-cyclodextrin) across SPR channels, generating real-time association and dissociation binding curves. With the exception of the oxidized FA hydroxyoctadecadienoic acid (HODE), all FA tested bound to CD36 with rapid association and dissociation kinetics similar to human serum albumin. In addition, FA increased oxLDL binding to CD36. To investigate whether FA affect CD36-mediated oxLDL uptake in live cells, we monitored fluorescent oxLDL (Dii-oxLDL) uptake using confocal microscopy. Addition of exogenous FA to serum-free media enhanced dose-dependent oxLDL uptake. Exceptions were ω-3 FA, which bound to CD36, and HODE, which did not bind to CD36, demonstrating FA structure-specific effects on a major function of CD36 and a new mechanistic link between atherosclerosis and high levels of FA in obese and Type-II diabetic individuals.

Non-equilibrium systems have no set method of analysis, and a wide array of dynamics can be present in such systems. In this work we present three very different non-equilibrium models, inspired by biological systems and phenomena, that we analyze through computational means to showcase both the range of dynamics encompassed by these systems, as well as various techniques used to analyze them. The first system we model is a surface plasmon resonance (SPR) cell, a device used to determine the binding rates between various species of chemicals. We simulate the SPR cell and compare these computational results with a mean-field approximation, and find that such a simplification fails for a wide range of reaction rates that have been observed between different species of chemicals. Specifically, the mean-field approximation places limits on the possible resolution of the measured rates, and such an analysis fails to capture very fast dynamics between chemicals. The second system we analyzed is an avalanching neural network that models cascading neural activity seen in monkeys, rats, and humans. We used a model devised by Lombardi, Herrmann, de Arcangelis et al. to simulate this system and characterized its behavior as the fraction of inhibitory neurons was changed. At low fractions of inhibitory neurons we observed epileptic-like behavior in the system, as well as extended tails in the avalanche strength and duration distributions, which dominate the system in this regime. We also observed how the connectivity of these networks evolved under the effects of different inhibitory fractions, and found the high fractions of inhibitory neurons cause networks to evolve more sparsely, while networks with low fractions maintain their initial connectivity. We demonstrated two strategies to control the extreme avalanches present at low inhibitory fractions through either the random or targeted disabling of neurons. The final system we present is a sparsely encoding convolutional neural network, a computational system inspired by the human visual cortex that has been engineered to reconstruct images inputted into the network using a series of "patterns" learned from previous images as basis elements. The network attempts to do so "sparsely," so that the fewest number of neurons are used. Such systems are often used for denoising tasks, where noisy or fragmented images are reconstructed. We observed a minimum in this denoising error as the fraction of active neurons was varied, and observed the depth and location of this minimum to obey finite-size scaling laws that suggest the system is undergoing a second-order phase transition. We can use these finite-size scaling relations to further optimize this system by tuning it to the critical point for any given system size. / Doctor of Philosophy / Non-equilibrium systems have no set method of analysis, and a wide array of dynamics can be present in such systems. In this work we present three very different non-equilibrium models, inspired by biological systems and phenomena, that we analyze through computational means to showcase both the range of dynamics encompassed by these systems, as well as various techniques used to analyze them. The first system we model is a surface plasmon resonance (SPR) cell, a device used to determine the binding rates between various species of chemicals. We simulate the SPR cell and compare these computational results with a mean-field approximation, and find that such a simplification fails for a wide range of reaction rates that have been observed between different species of chemicals. Specifically, the mean-field approximation places limits on the possible resolution of the measured rates, and such an analysis fails to capture very fast dynamics between chemicals. The second system we analyzed is an avalanching neural network that models cascading neural activity seen in monkeys, rats, and humans. We used a model devised by Lombardi, Herrmann, de Arcangelis et al. to simulate this system and characterized its behavior as the fraction of inhibitory neurons was changed. At low fractions of inhibitory neurons we observed epileptic-like behavior in the system, as well as extended tails in the avalanche strength and duration distributions, which dominate the system in this regime. We also observed how the connectivity of these networks evolved under the effects of different inhibitory fractions, and found the high fractions of inhibitory neurons cause networks to evolve more sparsely, while networks with low fractions maintain their initial connectivity. We demonstrated two strategies to control the extreme avalanches present at low inhibitory fractions through either the random or targeted disabling of neurons. The final system we present is a sparsely encoding convolutional neural network, a computational system inspired by the human visual cortex that has been engineered to reconstruct images inputted into the network using a series of “patterns” learned from previous images as basis elements. The network attempts to do so “sparsely,” so that the fewest number of neurons are used. Such systems are often used for denoising tasks, where noisy or fragmented images are reconstructed. We observed a minimum in this denoising error as the fraction of active neurons was varied, and observed the depth and location of this minimum to obey finite-size scaling laws that suggest the system is undergoing a second-order phase transition. We can use these finite-size scaling relations to further optimize this system by tuning it to the critical point for any given system size.

No description available.

Surface plasmon resonance (SPR) is a label-free, versatile and highly sensitive method for studying molecular interactions in real time. It is widely used by industry and academia alike in fields ranging from Alzheimer’s disease research to detection of heavy metals. In this review, studies published during the last 10 years using Biacore or other SPR instruments were compiled and compared. Trends were also identified in the field. Amine coupling was found to be the most common ligand strategy for proteins, and most SPR research related to the field of medicine. Furthermore, three main purposes of an SPR experiment were identified: To determine the affinity between a pair of molecules, kinetics between a pair of molecules or to detect a certain molecule in a solution. The results presented are often related to these three purposes, and are most often presented and evaluated in terms of kinetic, affinity and sensitivity constants. SPR can be used for studying a broad range of molecular interactions, and an overview was obtained by dividing up the field into different parts based on molecular interactions and SPR methods. The study of molecular interactions using SPR was divided into protein-protein interactions (PPIs), antibody-antigen, protein-biomolecule interactions, interactions between proteins and small molecules, and non-conventional SPR methods. Non-conventional SPR methods include localized surface plasmon resonance (LSPR) and SPR imaging (SPRi), which are both based on the same optical sensing principles as SPR.