A new sensor technology based on optical diffraction of visible light shows promise for sensing metal ions and other species that employ chemically-responsive metal oxide and conducting polymer grating elements. These materials undergo reversible redox processes upon interaction with a chemical analyte that subsequently induces changes in the materials refractive index. The two key design parameters of this sensing technique involve preparation of micropatterned sensor elements and the evaluation of appropriate wavelengths for detection of diffracted light. Much of the ability to “tune” a desired sensing response is dictated by the understanding of how factors of size, dimension, crystallinity, morphology, porosity, and heterogeneity influence analyte/sensor interactions (i.e., adsorption, binding, and transport). The effect of composition, structure, and morphology of MoO₃, WO₃, Moₓ W₁₋ₓO₃, IrOₓ and polyaniline grating materials on chemical, electrochemical and optical properties of these systems will be examined by a range of spectroscopic and electrochemical techniques. Comprehensive evaluation and correlation of materials’ optical properties to diffraction-based detection will advance understanding of the capabilities and limitations for the diffraction-based sensing methodology. This information can then used to determine optimal sensing parameters to improve detection limits, enhance sensitivity and increase the dynamic range for detection of model analytes. / text

This is a report on the fabrication and characterization of anisotropic, porous materials: functionally graded cellular and compositionally anisotropic aerogels. This new class of materials was fabricated by photopolymerization of selected regions of a homogeneous monolith using visible light. Visible light is not significantly absorbed and not significantly scattered by organic molecules and oxide nanoparticles in wet gels and it allows fabrication of deeply penetrating, well-resolved patterns. Simple variations of the exposure geometry allowed fabrication of a wide variety of anisotropic materials without requiring layers or bonding.

Silk proteins have provided a source of unique and versatile building blocks in the fabrication of biomedical devices for addressing a range of applications. Critical to advancing this field is the ability to establish an understanding of these proteins in their native and engineered states as well as in developing scalable processing strategies, which can fully exploit or enhance the stability, structure, and functionality of the two constituent proteins, silk fibroin and sericin. The research outlined in this dissertation focuses on the evolution in architecture and capability of silks, to effectively position a functionally-diverse, renewable class of silk materials within the rapidly expanding field of smart biomaterials. Study of the process of building macroscopic silk fibers provides insight into the initial steps in the broader picture of silk assembly, yielding biomaterials with greatly improved attributes in the assembled state over those of protein precursors alone. Self-organization processes in silk proteins enable their aggregation into highly organized architectures through simple, physical association processes. In this work, a model is developed for the process of aqueous behavior and aggregation, and subsequent two-dimensional behavior of natural silk sericin, to enable formation of a range of distinct, complex architectures. This model is then translated to an engineered system of fibroin microparticles, demonstrating the role of similar phenomena in creating autonomously-organized structures, providing key insight into future “bottom up” assembly strategies. The aqueous behavior of the water-soluble silk sericin protein was then exploited to create biocomposites capable of enhanced response and biocompatibility, through a novel protein-template strategy. In this work, sericin was added to the biocompatible and biodegradable poly(amino acid), poly(aspartic acid), to improve its pH-dependent swelling response. This work demonstrated the production of a range of porous scaffolds capable providing meaningful response to environmental stimuli, with application in tissue engineering scaffolds and biosensing technologies. Finally, to expand the capabilities of silk proteins beyond process-driven parameters to directly fabricate engineered architectures, a method for silk photopatterning was explored, enabling the direct fabrication of biologically-relevant structures at the micro and nanoscales. Using a facile bioconjugation strategy, native silk proteins could be transformed into proteins with a photoactive capacity. The well-established platform of photolithography could then be incorporated into fabrication strategies to produce a range of architectures capable of addressing spatially-directed material requirements in cell culture and further applications in the use of non-toxic, renewable biological materials.

L’objectif de ce travail est la réalisation de nouveaux microactionneurs à base depolymère conducteur électronique pouvant être envisagés pour une application denanodrone à ailes battantes.Deux réseaux interpénétrés de polymères (RIPs) POE/PTHF (poly(oxyded’éthylène)/polytétrahydrofurane) et POE/NBR (poly(oxyde d’éthylène/Nitrile Butadiene Rubber) ont été synthétisés et caractérisés. Par le contrôle de la synthèse de ces RIPs,une co-continuité de phase des deux réseaux partenaires a pu être obtenue. Ce travail a ainsi permis l’obtention de matériaux combinant les propriétés propres de chaque réseau, une bonne conductivité ionique (POE) et de bonnes propriétés mécaniques (PTHF et NBR). Les propriétés mécaniques du matériau ont permis de réaliser des matériaux polymères support d’électrolyte manipulables avec des épaisseurs inférieures à 10 μm.Des RIPs conducteurs ont pu être élaborés à partir de ces matériaux en incorporant le polymère conducteur électronique (poly(3,4-éthylènedioxythiophène) - PEDOT), par une dispersion non homogène à partir de la surface vers l’intérieur du film. Après incorporation d’un liquide ionique (le 1-éthyl-3-méthylimidazolium bis-(trifluorométhylsulfonyl)imide ou EMImTFSI), ces matériaux électroactifs ont été caractérisés et ont montré qu’ils pouvaient actionner à des fréquences élevées (100Hz) par rapport aux autres dispositifs de ce type.La mise en forme micrométrique de ces matériaux a ensuite été réalisée par un procédé propre aux microsystèmes. Les techniques de photolithographie et de gravure ionique réactive ont été adaptées et étudiées pour l’élaboration de ces microactionneurs. Un mécanisme de dégradation chimique du matériau a été proposé afin d’expliquer l’étape de gravure. Enfin, la caractérisation des microactionneurs a ensuite aussi été réalisée.La force développée par ces microactionneurs est de l’ordre du μN et le pourcentage de déformation est de 1,8 %. / The aim of this work is the realization of new microactuators based on electronicconducting polymer (ECP) for a flapping wing nano-aerial vehicle.Two Interpenetrating Polymer Networks (IPNs) PEO/PTHF(polyethyleneoxide/polytetrahydrofurane) and PEO/NBR (polyethyleneoxide/NitrileButadiene Rubber) were synthesized and characterized. By controlling the synthesis of these IPNs, a phase co-continuity of the two networks could be obtained. This work has enabled the production of materials combining the specific properties of each network, good ionic conductivity (PEO) and good mechanical properties (PTHF and NBR). The mechanical properties of the material allowed the synthesis of solid polymer electrolyte materials that can be elaborated and manipulated with thicknesses below 10 microns.The conducting IPNs are synthesized from previous IPNs in which the conductingpolymer (poly(3,4-ethylenedioxythiophene)), PEDOT, is non homogeneously dispersed i.e. the content decreases from the outside towards the center of the film.After incorporation of an ionic liquid (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide or EMImTFSI), these electroactive materials werecharacterized and showed their capacity to operate at frequency high frequency (100 Hz) compared to others systems in literature.The micrometer shaping of these materials was then carried out by processes specific to microsystems. Photolithography techniques and Reactive Ion Etching (RIE) have been adapted and designed for the development of microactuators. A chemical degradation mechanism of the material has been proposed to explain the etching step. Finally, the characterization of microactuators have been carried out. The force developed by these microactuators is in the range of N and the bending strain has reached 1.8%.

The chemistry of hafnium oxide based and materials are described in the context of ion exchange and lithography. HafSOx, represented by the composition HfO₂₋[subscript x](SO₄)x, is described to possess a significant capacity towards ion exchange in acidic and basic solutions, enabling films of HafSOx to be cleanly and readily be converted to oxide films by neutralization. The optical properties, composition and morphology of these oxide films are characterized. The fabrication of mixed metal oxide films is demonstrated via solution and ion exchange routes. This thesis also explores the photoresist chemistry of HafSOx resists. A photoreaction mechanism based on the decomposition of peroxide is proposed. In addition, the patterning of HafSOx films by 193 nm, extreme ultraviolet (EUV) and electron beam radiation is described, and the influence of composition on its photoresist properties is studied. / Graduation date: 2012

A primary objective of modern biology is to understand the molecular mechanisms which underlie cellular functions and a crucial part of this task is the ability to manipulate and analyze individual cells. As a result of interdisciplinary research, microfluidics may become the forefront of analytical methods used by biologists. This technology can be used to gain unprecedented opportunities for cell handling, lysis and investigation on a single cell basis. This thesis presents the development of a microfluidic device capable of selecting individual cells and performing selective electrical lysis of the plasma membrane, while verifying intactness of the nuclear membrane. The device is fabricated by an improved photolithography method and integrates molten solder as electrodes for lysis by a DC electric field. Quantification of lysis is accomplished by video and image analysis, and measurement of the rate of ion diffusion from the cell.

A primary objective of modern biology is to understand the molecular mechanisms which underlie cellular functions and a crucial part of this task is the ability to manipulate and analyze individual cells. As a result of interdisciplinary research, microfluidics may become the forefront of analytical methods used by biologists. This technology can be used to gain unprecedented opportunities for cell handling, lysis and investigation on a single cell basis. This thesis presents the development of a microfluidic device capable of selecting individual cells and performing selective electrical lysis of the plasma membrane, while verifying intactness of the nuclear membrane. The device is fabricated by an improved photolithography method and integrates molten solder as electrodes for lysis by a DC electric field. Quantification of lysis is accomplished by video and image analysis, and measurement of the rate of ion diffusion from the cell.

This thesis develops a novel photopatterning strategy for biomimetic scaffolds that enables spatial and biochemical control of engineered cellular architectures, such as the microvasculature. Intricate tools that allow for the three dimensional (3D) manipulation of biomaterial microenvironments will be critical for organizing cellular behavior, directing tissue formation, and ultimately, developing functional therapeutics to treat patients with critical organ failure. Poly(ethylene glycol) (PEG) based hydrogels, which without modification naturally resist protein adsorption and cellular adhesion, were utilized in combination with a two-photon laser patterning approach to covalently immobilize specific biomolecules in custom-designed, three-dimensional (3D) micropatterns. This technique, known as two-photon laser scanning lithography (TP-LSL), was shown in this thesis to possess the capability to micropattern multiple different biomolecules at modular concentrations into a single hydrogel microenvironment over a broad range of size scales with high 3D resolution. 3D cellular adhesion and migration were then explored in detail using time-lapse confocal microscopy to follow cells as they migrated along micropatterned tracks of various 3D size and composition. Further, in a valuable modification of TP-LSL, images from the endogenous microenvironment were converted into instructions to precisely direct the laser patterning of biomolecules within PEG-based hydrogels. 3D images of endogenous microvasculature from various tissues were directly converted into 3D biomolecule patterns within the hydrogel scaffold with precise pattern fidelity. While tissue engineers have previously demonstrated the formation of vessels through the encapsulation of endothelial cells and pericyte precursor cells within PEG-based hydrogels, the vessel structure had been random, uncoordinated, and therefore, ultimately non-functional. This thesis has utilized image guided TP-LSL to pattern biomolecules into a 3D structure that directs the organization of vessels to mimic that of the endogenous tissue vasculature. TP-LSL now stands as a valuable tool to control the microstructure of engineered cellular architectures, thereby providing a critical step in the development of cellularized scaffolds into functional tissues. Ultimately, this thesis develops new technologies that advance the field of regenerative medicine towards the goal of engineering viable organs to therapeutically treat the 18 patients who die every day waiting on the organ transplant list.

Nanochannel devices have been explored over the years with wide applications in bio/chemical analysis. With a dimension comparable to many bio-samples, such as proteins, viruses and DNA, nanochannels can be used as a platform to manipulate and detect such analytes with unique advantages. As a prerequisite to the development of nanochannel devices, various nanofabrication techniques have been investigated by many researchers for decades. In this dissertation, three different fabrication approaches for nanochannels are discussed, including a novel scanning coaxial electrospinning process, a heat-induced stretching approach and a standard contact photolithography process. The scanning coaxial electrospinning process is established based on conventional electrospinning process. A coaxial jet, with the motor oil as the core and spin-on-glass-coating/PVP solution as the shell, is deposited on the rotating collector as oriented coaxial nanofibers. These nanofibers are then annealed to eliminate the core material and form the hollow interior. Silica nanochannels with an inner diameter as small as 15 nm were obtained. The heat-induced stretching approach includes using commercially available fused silica tubings to create nanochannels by thermal deforming. This method and the electrospinning technique both focus on fabricate one-dimensional nanochannels with a circular opening. Fluorescent dye was used as a testing sample for single molecule detection and electrokinetic analysis in the resultant nanochannels. Another nanochannel device described in this dissertation has a deep-shallow step structure. It was fabricated by standard contact lithography, followed by etching and bonding. This device was applied as a powerful detection platform for surface-enhanced Raman spectroscopy (SERS). The experiment results proved that it is able to highly improve the sensitivity and efficiency of SERS. The SERS enhancement factor obtained from the device is 108. Moreover, the molecule enrichment effect of this device provides an extra 105 enhancement. The detection can be efficiently finished within minutes after simply loading the mixture of analytes solution and gold nanoparticles in the device. The sample consumption is in micro-liter range. Potential applications in diagnostics, prognositics and water pollutants detection could be achieved using this device.

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.