In this study, optical behavior of metal nanoparticles having dimensions smaller than the wavelength of visible light is studied experimentally and numerically. Gold (Au) and silver (Ag) nanoparticles are studied due to their superior optical properties when compared to other metals. A compact code based on Discrete Dipole Approximation (DDA) is developed to compute extinction efficiencies of nanoparticles with various different properties such as material, dimension and geometry. To obtain self consistent nanoparticle arrays with well defined geometries and dimensions, Electron Beam Lithography (EBL) technique is mainly used as the manufacturing method. Dose parameters required to produce nanoparticles with dimensions down to 50 nm over substrates with different electrical conductivities are determined. Beam current is found to affect the doseV size relation. The use of thin Au films as antistatic layer for e-beam patterning over insulating substrates is considered and production steps, involving instabilities due to contaminants introduced to the system during additional removal steps, are clarified. 4 nm thick Au layer is found to provide sufficient conductivity for e-beam patterning over insulating substrates. An optical setup capable of performing transmittance and reflectance measurements of samples having small areas patterned with EBL is designed. Sizes of the metal nanoparticles are determined by scanning electron microscope (SEM) and spectral data obtained using the optical setup is analyzed to find out the parameters affecting the localized surface plasmon resonances (LSPR). Arrays of particles with diameters between 50 &ndash / 200 nm are produced and optically analyzed. Size and shape of the nanoparticles are found to affect the resonance behavior. Furthermore, lattice constants of the particle arrays and surrounding medium are also shown to influence the reflectance spectra. Axes with different lengths in ellipsoidal nanoparticles are observed to cause distinguishable resonance peaks when illuminated with polarized light. Peak intensities obtained from both polarizations are observed to decrease under unpolarized illumination. Binary systems consisting of nanosized particles and holes provided better contrast for transmitted light.

Electrochemical biosensors are cost effective, fast and portable devices, which can determine the existence and amounts of chemicals in a specific medium. These devices have many potential applications in many fields such as determination of diseases, process and product control, environmental monitoring, and drug research. To realize these potentials of the devices, many studies are being carried out to increase their sensitivity, selectivity and long term stabilities. Surface modification studies with various types of particles (metal nano particles, carbon nano tubes etc.) can be count among these studies. Although zeolites and zeo-type materials are investigated for many years, they still hold interest on them due to their capabilities. By means of their chemical resistances, large surface areas, tailorable surface properties, and porous structures they can be applied in many applicational fields. In some recent studies, these properties are intended to be used in the field of biosensors. The purpose of the current study was to investigate the effect of zeolite nanoparticles on electrochemical biosensor performances. Firstly, several different procedures were investigated in order to find the best and optimum methodology to attach previously synthesized zeolites on Si wafer substrates for the first time. For this purpose, the ultrasonication, spin coating and direct attachment methods were used and their efficiencies were compared. Perfectly oriented, fully covering, zeolite monolayers are produced by direct attachment method. Successively produced zeolite thin films were then patterned with the help of Electron Beam Lithography technique to show the compatibility of coating methods to the CMOS technology. Combination of Direct Attachment and EBL techniques resulted well controlled zeolite monolayer patterns. Then zeolite modified electrochemical biosensors were tested for their performances. With these experiments it was intended to improve the selectivity, sensitivity and storage stabilities of standard electrochemical biosensors. Experiments, conducted with different types of zeolites, showed that zeolites have various effects on the performances of electrochemical biosensors. Amperometric biosensor response magnitudes have been doubled with the addition of Silicalites. Faster conductometric electrode responses were achieved with enzyme immobilization on zeolite film technique. Also it is seen that Beta type zeolites modified through different ion exchange procedures, resulted different responses in IS-FET measurements.

Zeolites are crystalline aluminosilicates which have highly ordered pore structures and high surface area. Also the tailorable surface properties, high ion-exchange capability, high chemical, thermal, and mechanical strength make these particles an important candidate for various application such as sensors, catalysis, dielectric materials, separation, and membrane technologies. Although zeolites have these unique properties, applications where zeolites are integrated into devices according to their application areas, are limited due to the powder form of the material. The purpose of the current study was to investigate the effect of zeolite nanoparticles on conductometric biosensor performance and cell viability measurements. Firstly, zeolite attachment on silicon surfaces was investigated by attaching silicalite and zeolite A nanoparticles onto the silicon substrates by direct attachment methodology in a closely packed monolayer form with perfect orientation and full coverage without using any chemical linker. Furthermore, the ability to pattern these zeolite crystals on silicon substrates with electron beam lithography and photolithography techniques was investigated. With the combination of electron beam lithography and direct attachment methodology, zeolite patterns were produced with feature sizes as small as a single silicalite nanoparticle thick line, that is approximately 500 nm. This approach has the ability of patterning very small features on silicon substrate, but the drawback is the long patterning time and lack of electron beam stability during long pattern formation process. Accordingly, it is almost impossible to form large patterns with electron beam lithography systems. Afterwards, to have full control on surfaces with differentiated areas on solid substrates, patterns of one type of zeolite crystals was formed on the monolayer of another type of zeolite layer with electron beam lithography for the first time. The same closed packed and highly oriented silicalite patterns were successfully formed on zeolite A monolayers and vice versa. Then photolithography technique was combined with direct attachment methodology to overcome the problem of the lack of total patterned area. With this technique, it was possible to pattern the whole silicon wafer in a couple of seconds, however the feature size of the zeolite patterns was limited with the infrastructures of the mask fabricated for photolithography studies. In this particular study, zeolite lines patterns with a minimum of 5 &micro / m thickness were prepared and the total patterned area was kept constant at 1 cm2. Similar to what was obtained by electron beam lithography study, zeolite A patterns were formed on silicalite monolayers with the minimum feature size of 5 &micro / m and vice versa. In the second part of the study, zeolite films were prepared on the transducers of conductometric biosensors using dip coating technique and named as Zeolite Coated Transducers (ZCT). Electrodes prepared using a mixture of zeolite and enzyme solution and then subjected to casting using glutaraldehyde were called Zeolite Membrane Transducers (ZMT). The operational and storage stabilities were determined to be in an acceptable range using ZCTs for conductometric urea biosensors. It was observed that using electrodes fabricated by the ZCT technique enhanced the biosensor signals up to two times and showed a rapid response after the addition of urea to the medium when it was compared with Standard Membrane Transducers (SMT). This enhancement can be explained by the lack of GA layer on top of the film, which acts as a diffusion barrier and inhibits the activity of the enzyme. On the second part of this conductometric biosensor study, effect of zeolite modification with methyl viologen (MV) and silver nanoparticles (Ag+ and Ag0), as well as the effect of changing Si/Al ratio was investigated with three different zeolite Beta particles which have Si/Al ratios of 40, 50, and 60. There were no significant effect of MV modification on ZMTs and there was no response observed with Ag+ and Ag0 modified zeolites. However, it was observed that conductometric responses increased with increasing Si/Al ratio for ZMTs. This behavior can be due to an increased hydrophobicity and/or the increasing acidic strength with the increasing Si/Al ratio within the zeolite crystals. Also ZCTs showed higher responses with respect to both SMTs and ZMTs. When compared with SMTs and ZMTs, ZCTs had higher reproducibility due to the controlled thickness of zeolite thin film by dip coating, and the controlled amount of enzyme adsorbed on this film. In the third part of the study, effect of zeolites on cell proliferation with MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. For that purpose, zeolite A, silicalite, and calcined forms of these zeolites were patterned with photolithography technique onto silicon wafers. Three different patterns prepared for this particular study, which has 0.125cm2, 0.08825cm2, and 0.04167cm2 zeolite patterned areas on 1 cm2 samples. In that way, not only the zeolite type and effect of calcination of zeolites, but also the effect of zeolite amount on MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. Silicalite coated samples were observed to have higher amount of cells than zeolite A coated samples after 24, 48, and 72 hours of incubation. This may be referred to the hydrophilic/hydrophobic properties, surface charge, and/or particle size of zeolites. Also it is observed that higher zeolite amount on samples resulted in an increase in the number of cells attached to the samples. There was also a significant increase in the number of cells upon using calcined silicalite samples. Accordingly, it can be hypothesized that zeolite pores result in an enhancement of protein adsorption and proliferation, even if this only occurs at the pore openings. On the other hand, there was no positive effect of calcining zeolite A. This result was expected since there is no structure directing agent used in synthesis procedure of zeolite A, which again supports the fact that pores might have some role in cell attachment.

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.

Device fabrication on multi walled carbon nanotubes (MWCNTs) using electrical beam lithography (EBL), electron beam induced deposition (EBID), ion beam induced deposition (IBID) methods was carried out, followed by device electrical characterization using a conventional probe station. A four-probe configuration was utilized to measure accurately the electrical resistivity of MWCNTs with similar results obtained from devices fabricated by different methods. In order to reduce the contact resistance of the beam deposited platinum electrodes, single step vacuum thermal annealing was performed. Microscopy and spectroscopy were carried out on the beam deposited electrodes to follow the structural and chemical changes occurring during the vacuum thermal annealing. For the first time, a core-shell type structure was identified on EBID Pt and IBID Pt annealed electrodes and analogous free standing nanorods previously exposed to high temperature. We believe this observation has important implications for transport properties studies of carbon materials. Apart from that, contamination of carbon nanostructure, originating from the device fabrication methods, was also studied. Finally, based on the observations of faster processing time together with higher yield and flexibility for device preparation, we investigated EBID to fabricate devices for other discrete carbon nanostructures.

This dissertation describes the development of a new method for increasing the resolution of the current protein microarray technology, down to the single molecule detection level. By using a technique called size-dependent self-assembly, different proteins can be bound to different sized fluorescent nanostructures, and then located on a patterned silicon substrate based on the sized pattern which is closest to the size of the bead diameter.The protein nanoarray was used to detect antibody-antigen binding, specifically anti-mouse IgG binding to mouse IgG. The protein nanoarray is designed with the goal of analyzing rare proteins. However, common proteins, such as IgG, are used in the initial testing of the array functionality. Mouse IgG, representing rare proteins, is conjugated to fluorescent beads and the beads are immobilized on a patterned silicon surface. Then anti-mouse IgG binds to the mouse IgG on the immobilized beads. The binding of the antibody, anti-mouse IgG, to the antigen, mouse IgG is determined by fluorescent signal attenuation.The first objective was to bind charged nanoparticles, conjugated with proteins, to an oppositely charged silicon substrate. Binding of negatively charged gold nanoparticles (AuNP), conjugated with mouse IgG, to a positively charged silicon surface was successful.The second objective was to demonstrate the method of size-dependent self-assembly at the nanometer scale (<100 >nm). Different-sized, carboxylated, fluorescent beads and AuNP, which were conjugated with proteins, were serially added to a patterned polymethyl methacrylate (PMMA) coated silicon surface. Size-dependent self-assembly was successfully demonstrated, down to the nanometer scale.The final objective was to obtain a signal from antibody-antigen binding within the protein array. Conjugated fluorescent beads were bound to e-beam patterns and signal attenuation was measured when the antibodies bound to the conjugated beads. The size-dependent self-assembly is a valuable new method that can be used for the detection and quantification of proteins.

This thesis addresses nanostructure fabrication techniques based on electron beam lithography, which is the most widely employed nanofabrication techniques for R&D and for the prototyping or production of photo-mask or imprint mold. The focus is on the study of novel resist and development process, as well as pattern transfer procedure after lithography. Specifically, this thesis investigates the following topics that are related to either electron beam resists, their development, or pattern transfer process after electron beam lithography: (1) The dry thermal development (contrary to conventional solvent development) of negative electron beam resists polystyrene (PS) to achieve reasonably high contrast and resolution. (2) The solvent development for polycarbonate electron beam resist, which is more desirable than the usual hot aqueous solution of NaOH developer, to achieve a low contrast that is ideal for grayscale lithography. (3) The fabrication of metal nanostructure by electron beam lithography and dry liftoff (contrary to the conventional liftoff using a strong solvent or aqueous solution), to achieved down to ~50 nm resolution. (4) The study a novel electron beam resist poly(sodium 4-styrenesulfonate) (sodium PSS) that is water soluble and water developable, to fabricate the feature size down to ~ 40 nm. And finally, (5) The fabrication of gold nanostructure on a thin membrane, which will be used as an object for novel x-ray imaging, where we developed the fabrication process for silicon nitride membrane, electroplating of gold, and pattern transfer after electron beam lithography using single layer resist and tri-layer resist stack.

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No description available.

Thin films of Teflon AF have been directly patterned by electron-beam lithography without the need for post exposure chemical development. The relationship between pattern depth and exposure dose was found to be linear over a wide range of doses. Pattern depth was also observed to be dependent on initial film thickness. Teflon AF can be directly patterned at doses similar to typical e-beam resists. High resolution features as small as ~200 nm have been resolved. FTIR measurements revealed that CF3 and fluorinated dioxole groups play a significant role in the patterning mechanism. Teflon AF films also exhibited an increase in refractive index upon exposure to the electron-beam. This property has been exploited in waveguiding applications. Waveguides in Teflon AF were patterned using direct electron beam lithography technique. Waveguides were clearly visible to the naked eye. Characterization in the visible region showed evidences of light guiding through the waveguides. However light could not cross the entire chip. Characterization in the infrared region revealed the slab mode even though individual waveguides were not detected.