Protein-protein and protein-molecule interactions are complicated phenomena due to the tendency of proteins to change shape and function in response to their environment. Protein aggregation whether onto surfaces or in solution, can pose numerous problems in industry. Surface plasmon resonance (SPR) devices and quartz crystal microbalances (QCM) are two real-time, label free methods that can be used to detect the interactions between molecules on surfaces. These devices often employ self-assembled monolayers (SAMs) to produce specific surfaces for studying protein-protein interactions. The objective of this work was to develop methodologies utilizing SPR to better understand protein-protein and protein-molecule interactions with possible applications in the food and separation industrial sectors. A very well characterized whey protein, β-lactoglobulin (BLG), is used in numerous applications in the food industry. BLG can undergo different types of self-aggregation due changes in external environment factors such as buffer strength, pH or temperature. In this work, a hydrophilic SAM was developed and used to study the interaction and non-specific adsorption of BLG and palmitic acid (PA), a molecule which is known to bind to BLG. It was found that PA tended to reduce BLG conformational changes once on the surface, resulting in a decrease in its surface adhesion. Fluorescent excitation emission matrices (EEM’s) using a novel fluorescence probe technique were utilized to detect protein on the surface as well as conformational changes on the surface of the sensor, although the extent these changes could not be quantified. Another whey protein, α-lactoglobulin (AL), was utilized as a surrogate protein to study the adsorption of colloidal/particulate and protein matter (CPP) extracted from filtration studies of river water. A large fraction of natural organic matter (NOM), the major foulant in membrane based water filtration, is CPP and protein. Understanding the interactions between these components is essential in abating NOM membrane fouling. Several SPR methods were investigated in order to verify the interactions. A mixture of AL and CPP particles in solution prevented the non-specific adsorption of AL to the SAM surface. This change in association was then detected through SPR. Fluorescent EEM’s of the sensor surface verified that CPP and AL bound to the surface. This finding has fundamental significance in the interpretation of NOM-based membrane fouling. To better understand the mechanisms behind non-specific adsorption, a mechanistic mathematical model was developed to describe the adsorption of BLGs onto the hydrophilic SAM. The resulting model performed well in terms of predicting adsorption based on SPR data. The model incorporated the monomer-dimer equilibrium of BLG in solution, highlighting the impact of protein aggregation on non-specific adsorption mechanisms. For future studies, improvement in fluorescent FOP surface scan methodology would help identify different protein/molecules and conformations on the surface.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

The high speed transfer of information in materials with dimensions below the sub-diffraction limit is essential for future technological developments. Metallic nanoparticle (NP) waveguides serve a unique role in efficient energy transfer in this size regime. Light may be confined to metallic structures and propagate along the surface of the waveguide via propagating plasmon waves known as surface plasmon polaritons (SPPs). Plasmon propagation of energy in metallic structures is not perfect however and damping losses from the waveguide material lead to a characteristic exponential decay in the plasmon near field intensity. This decay length is known as the propagation length and serves as an excellent metric to compare various waveguide materials and structures to one another at particular excitation wavelengths. This thesis presents recent work in the development of a novel measurement technique termed bleach imaged plasmon propagation (BlIPP). BlIPP uses the photobleaching property of fluorophores and far field fluorescence microscopy to probe the near-field intensity of propagating plasmons and determine the propagation length. The experimental setup, image analysis, conditions, and application of BlIPP are developed within this thesis and an in depth review of the 1-photon photobleaching mechanism is also investigated. The BlIPP method is used to investigate long plasmon propagation lengths along straight chains of tightly packed Au NPs through the coupling of light to sub-radiant propagating modes, where radiative energy losses are suppressed. The findings of this work reveal, experimentally, the importance of small gap distances for the propagation of energy. Complex chain architectures are then explored using BlIPP measurements of tightly packed straight and bent chains of spherical silver NPs. We observe the highly efficient propagation of energy around sharp corners with no additional bending losses. The findings of this thesis demonstrate the advantages and capabilities of using BlIPP propagation length measurement. Further, BlIPP is used to reveal the advantage of coupling light to sub-radiant modes of NP chains, which demonstrate the ability to guide light efficiently across long distances and around complex structures, bringing us a step closer to the goal of applying plasmonic devices and circuitry in ultra compact opto-electronic devices.

Plasmonic nanoparticles and their assembly have the potential to serve as a platform in practical applications such as photonics, sensing, and nano-medicine. To use plasmonic nanoparticles in these applications, it is important to understand their optical properties and find methods to control their optical response. Using polarization-sensitive dark-field spectroscopy to study self-assembled nanoparticle rings on substrates with different permittivities I show that the interaction between collective plasmon resonances and the substrate can control the spatial scattering image. Using liquid crystals as an active medium that can be controlled with an external electric field I show that the Fano resonance of an asymmetric plasmonic assembly can be actively controlled utilizing the polarization change of scattered light passing through the liquid crystal device. Furthermore, utilizing the strong electromagnetic field enhancement of coupled plasmonic “nanospikes” on the surface of gold nanoshells with a silica core, I show the use of single spiky nanoshells as surface-enhanced Raman spectroscopy substrates. Individual spiky nanoshells give surprisingly reproducible surface-enhanced Raman spectroscopy intensities with a low standard deviation compared to clusters of nanoparticles. In summary, the work presented here provides understanding of the plasmonic response for assembled nanoparticles on different substrates, illustrated a new method to actively control the optical response of plasmonic nanoparticles, and characterizes spiky nanoshells as surface-enhanced Raman scattering platform.

M-DNA is a complex formed between normal double-stranded DNA and the transition metal ions Zn2+, Ni2+, and Co2+ that is favoured by an alkaline pH. Previous studies have suggested that M-DNA formation involves replacement of the imino protons of G and T bases by the transition metal ions involved in forming the complex. Owing to the conductive properties of this unique DNA conformation, it has potential applications in nanotechnology and biosensing. This work was aimed at improving existing methods and developing new methods of characterizing M-DNA. The effects of base substitutions, particularly those of G and T, were evaluated in light of the proposed structure. Differences between M-DNA conformations induced by Zn2+ and Ni2+ were also investigated with a variety of techniques and compared to the effects of Cd2+ and Mg2+ on double-stranded DNA. M-DNA formation and stability were studied with an ethidium bromide (EtBr) based assay, M-DNA induced fluorescence quenching of DNA labelled with fluorescein and a compatible quenching molecule, isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR). Production of monoclonal antibodies against the conformation was also attempted but was unsuccessful. The EtBr-based assay showed Ni(II) M-DNA to be much more stable than Zn(II) M-DNA as a function of pH and in the presence of ethylenediaminetetraacetic acid. Sequence-dependency and the effect of base substitutions were measured as a function of pH. With regards to sequence, d(G)nd(C)n tracts were found to form the conformation most easily. Base substitutions with G and T analogues that lowered the pKa of these bases were found to stabilize M-DNA more strongly than other base substitutions. A combination of temperature-dependant EtBr and ITC assays showed M-DNA formation to be endothermic, and therefore entropy driven. The SPR studies demonstrated many qualitative differences between Zn(II) and Ni(II) M-DNA formation, allowed characterization of Zn2+, Ni2+, Cd2+, and Mg2+ complexes with single-stranded DNA, and provided unambiguous evidence that M-DNA formation results in very little denaturation of double-stranded DNA. Specifically, the SPR study showed Ni(II) M-DNA to be more stable than Zn(II) M-DNA in the absence of transition metal ions, but also showed that Ni(II) M-DNA required higher concentrations of Ni2+ than Zn2+ to fully form the respective M-DNA conformations. Finally, quenching studies demonstrated Zn(II) M-DNA formation over a pH range from 6.5 to 8.5 provided that a Zn2+:H+ ratio of roughly 105 was maintained. The Keq for this interaction was 1.3 x 10-8 with 1.4 H+ being liberated per base bair of M-DNA formed. These results support the proposed structural model of M-DNA, as lowering the pKa of the bases having titratable protons over the pH range studied facilitated M-DNA formation. The fact that Zn(II) M-DNA formation was observed by fluorescence quenching at any pH provided that a constant ratio of Zn2+:H+ was maintained was consistent with a simple mass-action interaction for M-DNA formation. The differences between Zn(II) and Ni(II) M-DNA formation show that although it requires a higher pH or transition metal ion concentration, Ni(II) M-DNA is more stable than Zn(II) M-DNA once formed. This difference could play an important role in applications of M-DNA which required modulation in the stability of the M-DNA conformation.

This dissertation consists of two topics. One is a "Multi-pass Fiber Optic Surface Plasmon Resonance Sensor (SPR)" and the other is a "Nano-metallic Surface Plasmon Lens." Since both topics involved surface plasmon, the title of this dissertation is named "Surface plasmon coupled sensor and nanolens." For a multi-pass fiber optic SPR sensor, a fiber optic 4-pass SPR sensor coupled with a field-assist capability for detecting an extremely low concentration of charged particles is first demonstrated. The multipass feature increases the sensitivity by a factor equal to the number of passes. The field-assist feature forces charged particles/molecules to the SPR surface, increasing the sensitivity by an additional factor of about 100. Overall, the sensitivity exceeds the one-pass SPR device by a factor of about 400. A 10 pM concentration of 47 nm diameter polystyrene (PS) latex beads and 1 ?M concentration of salt dissolved in DI water were detected within a few seconds by the combined system. The equivalent index resolution for atomic size corresponding to ionized chlorine in salt is 10-8. This technique offers the potential for sensitive and fast detection of biomolecules in a solution. Secondly, a 44-pass fiber optic surface plasmon resonance (SPR) sensor coupled with a field-assist capability for measurement of refractive index change due to positive and negative ions is shown. The field-assist feature forces ions to the SPR surface, causing the SPR signal response to change which reflects a decrease or increase in refractive index depending on whether positive or negative ions are being attracted to the surface. This technique offers the potential for the sensitive detection of cations and anions in a solution. For a nano-metallic surface plasmon lens, we analyze the transmission of a normally incident plane wave through an Ag/dielectric layered concentric ring structure using finite difference time domain (FDTD) analysis. The dependency of the transmission efficiency on the refractive index in slit is studied. The numerical analysis indicates that the focusing beyond diffraction limit is found even at the extended focal length comparable to the distance of 7" from the exit plane using a circularly polarized coherent plane wave, ?=405 nm. Especially, compared to an Ag-only structure, the Ag/ LiNbO3 structure amplifies the transmission power by a factor of 6. Therefore, this Ag/dielectric layered lens has the potential for significantly higher resolution imaging and optical data storage.

Understanding and manipulating nanosized particles is crucial for the advancement of nanotechnology research. Dependent light scattering of noble metals can be used to achieve new material responses that can be used in different applications. Dependent light scattering of nanoparticles allows the understanding of orientation and location of closely positioned particles. Besides, dependently scattering metallic particles create significantly enhanced near fields and high absorption rates when excited at their plasmon resonance. It is used for spectrally selective heating and melting of nanosized particles as a nanomanufacturing method. With numerical methods dependent scattering properties of particles can be obtained. In this study, the dependent optical absorption efficiencies of metallic nanoparticles are obtained with the newly developed Integrated Poynting Vector Approach (IPVA). This is used in conjunction with a numerical light scattering solution tool DDSCAT. Results indicate that IPVA and DDSCAT together can be used for the estimation of scattering and absorption of nanoparticles affected by the near field of other particles in their close vicinity. The method is suggested to be suitable for the understanding of physical mechanisms behind dependent scattering prior to experiments that require lots of effort and resources.

Optics has the inherent advantages of parallelism and wide bandwidths in processing information. However, the need to interface with electronics creates a bottleneck that eliminates many of these advantages. The proposed research explores novel optical devices and techniques to overcome some of these bottlenecks. To address parallelism issues we take a specific example of a content-addressable memory that can recognize images. Image recognition is an important task that in principle can be done rapidly using the natural parallelism of optics. However in practice, when presented with incomplete or erroneous information, image recognition often fails to give the correct answer. To address this problem we examine a scheme based on free-space interconnects implemented with diffractive optics. For bandwidth issues, we study possible ways to eliminate the electronic conversion bottleneck by exploring all-optical buffer memories and all-optical processing elements. For buffer memories we examine the specific example of slow light delay lines. Although this is currently a popular research topic, there are fundamental issues of the delay-time-bandwidth product that must be solved before slow light delay lines can find practical applications. For all-optical processing we examine the feasibility of constructing circuit elements that operate directly at optical frequencies to perform simple processing tasks. Here we concentrate on the simplest element, a sub-wavelength optical wire, along with a grating coupler to interface with conventional optical elements such as lenses and fibers. Even such a simple element as a wire has numerous potential applications. In conclusion, information processing by all-optical devices are demonstrated with an associative memory using diffractive optics, an all-optical delay line using room temperature slow light in photorefractive crystals, and a subwavelength optical circuit by surface plasmon effects.

The work presented in this dissertation suggests novel design of chemical plasmonic sensors which have been developed based on Localized Surface Plasmon Resonance (LSPR), and Surface-enhanced Raman scattering (SERS) phenomena. The goal of the study is to understand the SERS phenomena for 3D hybrid (organic/inorganic) templates and to design of the templates for trace-level detection of selected chemical analytes relevant to liquid explosives and hazardous chemicals. The key design criteria for the development of the SERS templates are utilizing selective polymeric nanocoatings within cylindrical nanopores for promoting selective adsorption of chemical analyte molecules, maximizing specific surface area, and optimizing concentration of hot spots with efficient light interaction inside nanochannels. The organic/inorganic hybrid templates are optimized through a comprehensive understanding of the LSPR properties of the gold nanoparticles, gold nanorods, interaction of light with highly porous alumina template, and the choice of physical and chemical attributes of the selective coating. Furthermore, novel method to assemble silver nanoparticles in 3D as the active SERS-active substrate has been demonstrated by uniform, in situ growth of silver nanoparticles from electroless deposited silver seeds excluding any adhesive polymer layer on template. This approach can be the optimal for SERS sensing applications because it is not necessary to separate the Raman bands of the polyelectrolyte binding layer from those of the desired analyte. The fabrication method is an efficient, simple and fast way to assemble nanoparticles into 3D nanostructures. Addressable Raman markers from silver nanowire crossbars with silver nanoparticles are also introduced and studied. Assembly of silver nanowire crossbar structure is achieved by simple, double-step capillary transfer lithography. The on/off SERS properties can be observed on silver nanowire crossbars with silver nanoparticles depending on the exact location and orientation of decorated silver nanoparticles nearby silver nanowire crossbars. As an alternative approach for the template-assisted nanostructure design, porous alumina membrane (PAM) can be utilized as a sacrificial template for the fabrication of the nanotube structure. The study seeks to investigate the design aspects of polymeric/inorganic hybrid nanotube structures with plasmonic properties, which can be dynamically tuned by external stimuli such as pH. This research suggests several different organic/inorganic nanostructure assemblies by various template-assisted techniques. The polymeric/inorganic hybrid nanostructures including SERS property, pH responsive characteristics, and large surface area will enable us to understand and design the novel chemical plasmonic sensors.

Moderne Methoden der Oberflächenbehandlung können Oberflächen mit besonderen Eigenschaften versehen. Diese Eigenschaften werden zunehmend durch ultradünne Schichten mit Schichtdicken von einigen Nanometern erzeugt, da mit minimalem Materialaufwand definierte Resultate erreichbar sind. Die meisten Metalle überziehen sich mit einer Oxidschicht, deren Eigenschaften von den herrschenden Umgebungsbedingungen bestimmt werden. Diese Oxidschicht bildet die Oberfläche des Festkörpers, und weist andere Eigenschaften auf als der Festkörper selbst. Darüber hinaus beeinflussen die Rauhigkeit sowie eventuell vorliegende Legierungsbestandteile die Oberflächenbeschaffenheit. Besonders geeignet zum Erzeugen ultradünner oder monomolekularer Schichten ist der Prozess der Selbstorganisation, bei dem man sich zu Nutze macht, dass oberflächenaktive Moleküle mit sich selbst und einem Substrat in Wechselwirkung treten können. Zum Verständnis der ablaufenden Vorgänge ist die Kenntnis der Prozesskinetik sowie die Charakterisierung der Substratoberfläche vor und nach der Adsorption erforderlich. Die Größenverhältnisse zwischen den adsorbierten Molekülen und der Rauheit der Oberfläche erschweren die Charakterisierung der vorliegenden Ordnung und Orientierung der erzeugten dünnen Schichten. In dieser Arbeit sind Untersuchung des Schichtbildungsverhaltens und die Charakterisierung der erzeugten Schichten aus Phosphon- und Phosphorsäurederivaten in Abhängigkeit verschiedener Eigenschaften der Substratoberflächen vorgenommen worden. Dabei kamen oberflächensensitive Methoden wie AFM, REM, SPR und XPS zum Einsatz. Es konnte gezeigt werden, dass sich die untersuchten Moleküle wie erwartet auf den Oberflächen orientieren und dabei einen Bedeckungsgrad von etwa 60% erreichen. Der Einfluss von unterschiedlichen Vorbehandlungsmethoden konnte ebenso charakterisiert werden.