The technique of single particle Total Internal Reflection Microscopy (TIRM) has been used to study the scattering intensity from levitated microspheres. TIRM can be used to monitor the separation between microscopic spheres immersed in liquid (water in our case) and a surface with nm resolution. In the technique, microspheres scatter light when the evanescent waves are incident upon them. The intensity of the scattered light is directly related to the height above the surface and allows determination of the height. From the separation distance histograms, the interaction between the microsphere and interface may be characterized with a force resolution in the range of 0.01 picoNewtons. Such a system can be applied to the measurement of biomolecular interactions biomolecules attached to the microsphere and the surface. The intensity and scattering pattern of this light has been modeled using a modified Mie theory which accounts for the evanescent nature of the incident light. Diffusing Colloidal Probe Microscopy (DCPM) is an extension of the TIRM technique that simultaneously monitors multiple microsphere probes. The use of multiple probes introduces the issue of probe polydispersity. When measured at the surface, a variation in scattered light intensity of nearly one order of magnitude has been observed from a purchased microsphere sample. Thus the polydisperse collection of microspheres adds significant complexity to the scattered light signal. It is hypothesized that the dependence of the total scattered light intensity on microsphere size accounts for the scattered intensity distribution in a polydisperse microsphere sample. Understanding this variation in the scattered light with microsphere size will allow improved characterization of the microsphere/surface separation. Additionally, larger microspheres have the ability to resonantly confine light and produce spectrally narrow Whispering Gallery Modes (WGMs). It is hypothesized that WGMs may be excited in microspheres with the DCPM system. These modes may be used as a refractometric biosensor with high sensitivity to local refractive index changes on the surface of the microsphere. This research involves modeling scattered intensity distributions for polydispersed collections of microspheres based on modified Mie theory. The theoretical results are compared to experimentally obtained results and found to qualitatively explain the scattered light intensity distribution in a multiple probe DCPM system. This is an important result suggesting that microsphere size variation plays a major role in determining the distribution of scattered intensity in multiple microsphere probe systems. This work also suggests that it may be possible to excite such WGMs in a DCPM system. The introduction of WGMs would enable refractometric biosensing in such evanescent mode systems.

The technique of single particle Total Internal Reflection Microscopy (TIRM) has been used to study the scattering intensity from levitated microspheres. TIRM can be used to monitor the separation between microscopic spheres immersed in liquid (water in our case) and a surface with nm resolution. In the technique, microspheres scatter light when the evanescent waves are incident upon them. The intensity of the scattered light is directly related to the height above the surface and allows determination of the height. From the separation distance histograms, the interaction between the microsphere and interface may be characterized with a force resolution in the range of 0.01 picoNewtons. Such a system can be applied to the measurement of biomolecular interactions biomolecules attached to the microsphere and the surface. The intensity and scattering pattern of this light has been modeled using a modified Mie theory which accounts for the evanescent nature of the incident light. Diffusing Colloidal Probe Microscopy (DCPM) is an extension of the TIRM technique that simultaneously monitors multiple microsphere probes. The use of multiple probes introduces the issue of probe polydispersity. When measured at the surface, a variation in scattered light intensity of nearly one order of magnitude has been observed from a purchased microsphere sample. Thus the polydisperse collection of microspheres adds significant complexity to the scattered light signal. It is hypothesized that the dependence of the total scattered light intensity on microsphere size accounts for the scattered intensity distribution in a polydisperse microsphere sample. Understanding this variation in the scattered light with microsphere size will allow improved characterization of the microsphere/surface separation. Additionally, larger microspheres have the ability to resonantly confine light and produce spectrally narrow Whispering Gallery Modes (WGMs). It is hypothesized that WGMs may be excited in microspheres with the DCPM system. These modes may be used as a refractometric biosensor with high sensitivity to local refractive index changes on the surface of the microsphere. This research involves modeling scattered intensity distributions for polydispersed collections of microspheres based on modified Mie theory. The theoretical results are compared to experimentally obtained results and found to qualitatively explain the scattered light intensity distribution in a multiple probe DCPM system. This is an important result suggesting that microsphere size variation plays a major role in determining the distribution of scattered intensity in multiple microsphere probe systems. This work also suggests that it may be possible to excite such WGMs in a DCPM system. The introduction of WGMs would enable refractometric biosensing in such evanescent mode systems.

Immobilization of photosynthetic cultures has been used to generate biofuels and high value compounds through direct conversion of CO2 and water using sunlight. Compared with suspended cultures, immobilized bacteria can achieve much higher densities resulting in greater areal productivity. Limitations exist however, on the density that can be reached without compromising access to light and other nutrients. In this thesis an optofluidic approach to overcoming the challenge of light delivery to high density cultures of cyanobacteria is described and proof of concept experiments presented. This approach uses optical waveguides to deliver light to cells through bacterial interaction with the evanescent field and is tailored to meet each cell's need for light and nutrients. Experiments presented here demonstrate biofilm proliferation in the presence of evanescent fields. Illumination of surfaces by surface plasmon enhanced evanescent fields is also shown to be an effective and potentially useful technique to grow biofilms within optofluidic architectures.

In the last decade, design and application of negative materials have been one of the most interesting subjects in the electromagnetic research. The extraordinary properties of double negative (DNG) and single negative (SNG) materials have been studied extensively over this period. In this thesis, one of the unusual properties of negative materials, the evanescent amplification, is used to improve the sensitivity of the near field probes. The effect of placing DNG and SNG layers between the near field probes and the targets are investigated theoretically. A sensitivity definition is introduced for evanescent probes and it is shown using quantitative measures that the sensitivity can be increased using DNG and SNG materials for a target in vacuum and for a buried target. The electromagnetic loss of the negative materials and the mismatch between the material properties of the host medium and DNG and SNG materials are studied. Using an unmatched DNG layer or SNG layer enhances the sensitivity within an evanescent spectrum range while a lossless and matched DNG layer improves the sensitivity of entire evanescent spectrum. The idea of using negative materials is implemented over conventional near field probes by numerical experiments. Sensitivities of open-ended waveguides and open-ended coaxial lines for a specific application are studied in the presence of negative materials. In the case of precursor pitting detection on airplane bodies, the sensitivity of an open-ended waveguide probe is increased by 35 times for a λ/10 sized cubic crack. It is also shown that the negative material increases the quality of the image generated by the probe. The sensitivity improvement is also verified for an open-ended coaxial line. A 11 times improvement is achieved for a similar detection practice, with a λ/20 sized crack. The effect of coaxial line size and the dielectric material on the sensitivity enhancement are studied. The improvement is studied theoretically and numerically for an electrically small dipole. Theoretical studies show that when a small dipole is placed within a spherical shell made of DNG materials, the antenna parameters of the dipole becomes more sensitive to the position of a target placed outside the negative material shell. The field distribution generated by a small dipole in a multilayered spherical medium is studied for this purpose. Numerical analysis of a small dipole placed next to a planar DNG layer is presented. The DNG layer increases the sensitivity of the dipole due to a λ/30 sized metallic target by 5.5 times. To provide experimental verification, the sensitivity of an electrically small loop is studied. SNG materials with a negative permeability around 1.25 GHz are designed using modified split ring resonators (MSRR). By using the effective parameters of the designed structure, a sensitivity improvement of 10 times is achieved numerically. The improvement is verified using fabricated MSRR structures. The sensitivity of the small loop is enhanced by 9 times for a λ/12.2 sized metallic target. The sensitivity improvements are achieved within the frequency band where the MSRR structures behave as a μ-negative SNG material.

In the last decade, design and application of negative materials have been one of the most interesting subjects in the electromagnetic research. The extraordinary properties of double negative (DNG) and single negative (SNG) materials have been studied extensively over this period. In this thesis, one of the unusual properties of negative materials, the evanescent amplification, is used to improve the sensitivity of the near field probes. The effect of placing DNG and SNG layers between the near field probes and the targets are investigated theoretically. A sensitivity definition is introduced for evanescent probes and it is shown using quantitative measures that the sensitivity can be increased using DNG and SNG materials for a target in vacuum and for a buried target. The electromagnetic loss of the negative materials and the mismatch between the material properties of the host medium and DNG and SNG materials are studied. Using an unmatched DNG layer or SNG layer enhances the sensitivity within an evanescent spectrum range while a lossless and matched DNG layer improves the sensitivity of entire evanescent spectrum. The idea of using negative materials is implemented over conventional near field probes by numerical experiments. Sensitivities of open-ended waveguides and open-ended coaxial lines for a specific application are studied in the presence of negative materials. In the case of precursor pitting detection on airplane bodies, the sensitivity of an open-ended waveguide probe is increased by 35 times for a λ/10 sized cubic crack. It is also shown that the negative material increases the quality of the image generated by the probe. The sensitivity improvement is also verified for an open-ended coaxial line. A 11 times improvement is achieved for a similar detection practice, with a λ/20 sized crack. The effect of coaxial line size and the dielectric material on the sensitivity enhancement are studied. The improvement is studied theoretically and numerically for an electrically small dipole. Theoretical studies show that when a small dipole is placed within a spherical shell made of DNG materials, the antenna parameters of the dipole becomes more sensitive to the position of a target placed outside the negative material shell. The field distribution generated by a small dipole in a multilayered spherical medium is studied for this purpose. Numerical analysis of a small dipole placed next to a planar DNG layer is presented. The DNG layer increases the sensitivity of the dipole due to a λ/30 sized metallic target by 5.5 times. To provide experimental verification, the sensitivity of an electrically small loop is studied. SNG materials with a negative permeability around 1.25 GHz are designed using modified split ring resonators (MSRR). By using the effective parameters of the designed structure, a sensitivity improvement of 10 times is achieved numerically. The improvement is verified using fabricated MSRR structures. The sensitivity of the small loop is enhanced by 9 times for a λ/12.2 sized metallic target. The sensitivity improvements are achieved within the frequency band where the MSRR structures behave as a μ-negative SNG material.

The technique of single particle Total Internal Reflection Microscopy (TIRM) has been used to study the scattering intensity from levitated microspheres. TIRM can be used to monitor the separation between microscopic spheres immersed in liquid (water in our case) and a surface with nm resolution. In the technique, microspheres scatter light when the evanescent waves are incident upon them. The intensity of the scattered light is directly related to the height above the surface and allows determination of the height. From the separation distance histograms, the interaction between the microsphere and interface may be characterized with a force resolution in the range of 0.01 picoNewtons. Such a system can be applied to the measurement of biomolecular interactions biomolecules attached to the microsphere and the surface. The intensity and scattering pattern of this light has been modeled using a modified Mie theory which accounts for the evanescent nature of the incident light. Diffusing Colloidal Probe Microscopy (DCPM) is an extension of the TIRM technique that simultaneously monitors multiple microsphere probes. The use of multiple probes introduces the issue of probe polydispersity. When measured at the surface, a variation in scattered light intensity of nearly one order of magnitude has been observed from a purchased microsphere sample. Thus the polydisperse collection of microspheres adds significant complexity to the scattered light signal. It is hypothesized that the dependence of the total scattered light intensity on microsphere size accounts for the scattered intensity distribution in a polydisperse microsphere sample. Understanding this variation in the scattered light with microsphere size will allow improved characterization of the microsphere/surface separation. Additionally, larger microspheres have the ability to resonantly confine light and produce spectrally narrow Whispering Gallery Modes (WGMs). It is hypothesized that WGMs may be excited in microspheres with the DCPM system. These modes may be used as a refractometric biosensor with high sensitivity to local refractive index changes on the surface of the microsphere. This research involves modeling scattered intensity distributions for polydispersed collections of microspheres based on modified Mie theory. The theoretical results are compared to experimentally obtained results and found to qualitatively explain the scattered light intensity distribution in a multiple probe DCPM system. This is an important result suggesting that microsphere size variation plays a major role in determining the distribution of scattered intensity in multiple microsphere probe systems. This work also suggests that it may be possible to excite such WGMs in a DCPM system. The introduction of WGMs would enable refractometric biosensing in such evanescent mode systems.

The technique of single particle Total Internal Reflection Microscopy (TIRM) has been used to study the scattering intensity from levitated microspheres. TIRM can be used to monitor the separation between microscopic spheres immersed in liquid (water in our case) and a surface with nm resolution. In the technique, microspheres scatter light when the evanescent waves are incident upon them. The intensity of the scattered light is directly related to the height above the surface and allows determination of the height. From the separation distance histograms, the interaction between the microsphere and interface may be characterized with a force resolution in the range of 0.01 picoNewtons. Such a system can be applied to the measurement of biomolecular interactions biomolecules attached to the microsphere and the surface. The intensity and scattering pattern of this light has been modeled using a modified Mie theory which accounts for the evanescent nature of the incident light. Diffusing Colloidal Probe Microscopy (DCPM) is an extension of the TIRM technique that simultaneously monitors multiple microsphere probes. The use of multiple probes introduces the issue of probe polydispersity. When measured at the surface, a variation in scattered light intensity of nearly one order of magnitude has been observed from a purchased microsphere sample. Thus the polydisperse collection of microspheres adds significant complexity to the scattered light signal. It is hypothesized that the dependence of the total scattered light intensity on microsphere size accounts for the scattered intensity distribution in a polydisperse microsphere sample. Understanding this variation in the scattered light with microsphere size will allow improved characterization of the microsphere/surface separation. Additionally, larger microspheres have the ability to resonantly confine light and produce spectrally narrow Whispering Gallery Modes (WGMs). It is hypothesized that WGMs may be excited in microspheres with the DCPM system. These modes may be used as a refractometric biosensor with high sensitivity to local refractive index changes on the surface of the microsphere. This research involves modeling scattered intensity distributions for polydispersed collections of microspheres based on modified Mie theory. The theoretical results are compared to experimentally obtained results and found to qualitatively explain the scattered light intensity distribution in a multiple probe DCPM system. This is an important result suggesting that microsphere size variation plays a major role in determining the distribution of scattered intensity in multiple microsphere probe systems. This work also suggests that it may be possible to excite such WGMs in a DCPM system. The introduction of WGMs would enable refractometric biosensing in such evanescent mode systems.

This thesis explores the application of coiled sapphire multimode optical fibers for evanescent wave chemical sensing in both the visible spectrum and the near infrared. As has been suggested in the literature pertaining to silica fibers, bending converts low-order modes to high order ones, which leads to more evanescent absorption and thus a more sensitive chemical detector. By coiling the fiber many times, it was expected that even greater sensitivity would be attained. Experiments were performed to investigate the sensor response to different solutions and to characterize this response. In the first of three experiments, the large absorption peak of water at 3μm was examined in order to compare the sensitivity of a straight fiber versus a coiled one. In the second experiment, the effect of increasing the number of coils was investigated, as was the response of the sensor to varying concentrations of water in heavy water. In the third experiment, methylene blue dye was used to investigate the extent of adsorption of dye molecules on the sapphire fiber and its persistence

A broadband coupling approach applied to a single mode, sol-gel, planar integrated optical waveguide (IOW) was used to create a multichannel attenuated total reflection (ATR) spectrometer. Initial attempts to create an achromatic coupling element for sol-gel waveguides, based upon previous work applied to vacuum deposited glass devices, did not lead to an easily achievable design. Instead a simplified, non-achromatic approach based upon impinging an incident light beam with a large numerical aperture onto an incoupling prism was used. This simplified broadband coupling approach was used to create a sol-gel IOW-ATR spectrometer that transmitted light down to at least 400 nm, and produced a measurable bandwidth of ~ 250 nm; both phenomena are marked improvements upon the capabilities of previously reported devices. An experimental demonstration of this device proved it capable of measuring the visible spectrum of a thin film of horse heart cytochrome c adsorbed to the sol-gel surface at a submonolayer coverage. The broadband spectral capabilities of this sol-gel device were also used to experimentally validate a new method for determining the angular orientation of molecules bound to an arbitrary waveguide surface. In addition to the sol-gel IOW work, the simplified broadband coupling approach was applied to a previously reported multilayered electroactive waveguide device, which was used to collect electrically modulated, broadband spectra for thin films of cytochrome c, as well as a dicarboxyferrocene moiety. Both of these IOW-ATR spectrometers represent improved tools for probing the near-surface chemical environments of molecular assemblies.

Photosynthetic biofilms have much higher cell density than suspended cultures and when grown in a stacked waveguide configuration, can have orders of magnitude higher areal productivity. Evanescent and plasmonic growth of biofilm cultures have been demonstrated, solving issues with light penetration impeding growth, but thus far the technology has been limited to biofuel production applications. In this thesis, plasmonically excited cyanobacterial biofilms are used to produce electrical power in a photosynthetic-plasmonic-voltaic device. This approach uses red lasers to deliver light to cells via an optical waveguide through the generation of surface plasmons at the interface between a metal and dielectric, in this case a glass-gold-air interface. This gold film serves a dual purpose as a current collector for electrons generated at the cell surface. Experiments presented here demonstrate positive power output light response under both direct light and plasmonic excitation and produced equivalent power output of 6 uW/m2 under similar light power intensities.