The development of a waterborne pathogen detection method that is rapid, multiplex, sensitive, and specific, would be of great assistance for water treatment facilities and would help protect water consumers from harmful pathogens. Here we have utilized surface enhanced Raman spectroscopy (SERS) in a sensitive multiplex pathogen detection method. Two strategies are proposed herein, one that utilizes SERS antibody labels and one that measures the intrinsic SERS signal of organisms. For the SERS label strategy, gold nanoparticles are conjugated with antibodies specific to Cryptosporidium parvum and Giardia lamblia and with organic dye molecules. The dye molecules, rhodamine B isothiocyanate (RBITC) and malachite green isothiocyanate (MGITC) were surface enhanced by the gold nanoparticles resulting in unique fingerprint SERS spectra. The SERS label method was successful in detecting G. lamblia and C. parvum simultaneously. The method was subsequently coupled with a filtration step to both concentrate and capture cysts on a flat surface for detection. Raman mapping across the filter membrane detected ~95% of the spiked cysts in the optimized system. In the second type of strategy, intrinsic virus SERS signals were detected with silver nanoparticles for enhancement. Principal component analysis performed on the spectra data set resulted in the successful differentiation of MS2 and PhiX174 species and also for the differentiation of viable virus samples and inactivated virus samples. / Ph. D.

Understanding the different igneous processes that magmas undergo is important for a variety of reasons including potential hazards associated with volcanoes in populated regions, magmatic hydrothermal ore deposition, and tectonic processes. One method of obtaining geochemical data that can help constrain petrogenetic processes is through the study of melt and fluid inclusions. The research presented here examines melt inclusions through experimental, analytical and field studies to better understand igneous petrogenesis. One potential problem associated with melt inclusions is water-loss during laboratory heating. A Raman spectroscopic technique was developed to determine water contents of silicate glasses, and this technique was applied to monitor water loss from natural melt inclusions that were heated for varying lengths of time. The results suggest that water loss is insignificant when heated for less than 12 hours but significant water loss can occur with longer duration heating. The distribution of trace elements between silicate melts and phenocrysts growing from that melt can constrain igneous processes such as fractional crystallization, assimilation, and partial melting. Partition coefficients were determined for syngenetic clinopyroxene, orthopyroxene, and plagioclase in equilibrium with a dacitic melt using the Melt Inclusion-Mineral (MIM) technique. Melt inclusion chemistry is the same regardless of mineral host phase, suggesting that the melt inclusions have not been subjected to re-equilibration processes or boundary layer development. Partition coefficients from this study are similar but typically lower than published values. Three closely-spaced monogenetic eruptive units from the active Campi Flegrei volcanic system (Italy) with similar eruptive styles were examined to better understand the evolution of the magmatic system. Results suggest fractional crystallization as the dominant process taking place over time but that magma mixing was significant for one of the eruptions. Trace element geochemical data suggest a mixed magma source of within-plate and volcanic arc components, and still retain a T-MORB signature from the subducting slab. / Ph. D.

The system H₂O-CH₄ is found in a variety of geological environments in the earth’s crust, from sedimentary basins to low grade metamorphic terrains. Knowledge of the PressureVolume-Temperature-Composition (PVTX) properties of the H₂O-CH₄ system is necessary to understand the role that these fluids play in different geological environments. In this study the properties of the H₂O-CH₄ fluid system at elevated temperatures and pressures has been investigated experimentally to determine the PVTX properties of H₂O-CH₄ fluids in the P-T range equivalent to late diagenetic to low grade metamorphic environments, and XCH₄≤4mol%. A study has also been conducted to determine methane hydrate stability over the temperature range of -40~20°C. Synthetic fluid inclusions were employed in both studies as miniature autoclaves. Experimental data for the PVTX properties of H₂O-CH₄ fluids under late diagenetic to low grade metamorphic conditions was used to calculate the slopes of isoTh lines (the line connecting the P-T conditions of the inclusions at formation and at homogenization) at different PTX conditions. An empirical equation to describe the slope of iso-Th line as a function of homogenization temperature and fluid composition was developed. The equation is applicable to natural H₂O-CH₄ fluid inclusions up to 500°C and 3 kilobars, for fluid compositions ≤4 mol% CH₄. The Raman peak position of CH₄ gas is a function of the pressure and temperature. This relationship was used to determine the pressure along the methane hydrate stability curve in the H₂O-CH₄ system. The combined synthetic fluid inclusion, microthermometry and Raman spectroscopy method is a novel experimental approach to determine the P-T stability conditions of methane hydrates. The method is fast compared to conventional methods, and has the potential to be applied to study other gas hydrate systems. / Ph. D.

Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique that combines molecular specificity of vibrational fingerprints offered by Raman spectroscopy with single-molecule detection sensitivity from plasmonic hotspots of noble metal nanostructures. Label-free SERS has attracted tremendous interest in bioanalysis over the last two decades due to minimal sample preparation, non-invasive measurement without water background interference, and multiplexing capability from rich chemical information of narrow Raman bands. Nevertheless, significant challenges should be addressed to become a widely accepted technique in bio-related communities. In this dissertation, limitations from different aspects (performance, reliability, and analysis) are articulated with state-of-the-art, followed by how introduced works resolve them. For high SERS performance, SERS substrates consisting of vertically-stacked multiple metal-insulator-metal layers, named nanolaminate, were designed to simultaneously achieve high sensitivity and excellent uniformity, two previously deemed mutually exclusive properties. Two unique factors of nanolaminate SERS substrates were exploited for the improved reliability of label-free in situ classification using living cancer cells, including background refractive index (RI) insensitivity from 1.30 to 1.60, covering extracellular components, and 3D protruding nanostructures that can generate a tight nano-bio interface (e.g., hotspot-cell coupling). Discrete nanolamination by new nanofabrication additionally provides optical transparency, offering backside-excitation, thereby label-free glucose sensing on a skin-phantom model. Towards reliable quantitative SERS analysis, an electronic Raman scattering (ERS) calibration method was developed. ERS from metal is omnipresent in plasmonic constructs and experiences identical hotspot enhancements. Rigorous experimental results support that ERS can serve as internal standards for spatial and temporal calibration of SERS signals with significant potential for complex samples by overcoming intrinsic limitations of state-of-art Raman tags. ERS calibration was successfully applied to label-free living cell SERS datasets for classifying cancer subtypes and cellular drug responses. Furthermore, dual-recognition label-SERS with digital assay revealed improved accuracy in quantitative dopamine analysis. Artificial neural network-based advanced machine learning method was exploited to improve the interpretability of bioanalytical SERS for multiple living cell responses. Finally, this dissertation provides future perspectives with different aspects to design bio-interfaced SERS devices for clinical translation, followed by guidance for SERS to become a standard analytical method that can compete with or complement existing technologies. / Doctor of Philosophy / In photonics, metals were thought to be not very useful, except mirrors. However, at a length scale smaller than wavelength, it has been realized that metallic structures can provide unique ways of light manipulation. Maxwell's equations show that an interface between dielectric and metal can support surface plasmons, resulting in collective oscillations of electrons and light confinement. Surface-enhanced Raman spectroscopy (SERS) is a sensing technique that combines enhanced local fields arising from plasmon excitation with molecular fingerprint specificity of vibrational Raman spectroscopy. The million-fold enhancement of Raman signals at hotspots has driven an explosion of research, providing tons of publications over the last two decades with a broad spectrum of physical, chemical, and biological applications. Nevertheless, significant challenges should be addressed for SERS to become a widely accepted technique, especially in bio-related communities. In this dissertation, limitations from different aspects (performance, reliability, and analysis) are articulated with state-of-the-art, followed by how innovative strategies addressed them. Each chapter's unique approach consists of a combination of five aspects, including nanoplasmonics, nanofabrication, nano-bio interface, cancer biology, statistical machine learning. First, high-performance SERS substrates were designed to simultaneously achieve high sensitivity and excellent uniformity, two previously deemed mutually exclusive properties, by vertically stacking multiple metal-insulator-metal layers (i.e., nanolaminate). Their 3D protruding nanotopography and refractive-index-insensitive SERS response enabled label-free in situ classification of living cancer cells. Tweaked nanofabrication produced discrete nanolamination with optical transparency, enabling label-free glucose sensing on a skin phantom. Towards reliable quantitative SERS analysis, an electronic Raman scattering (ERS) calibration method was developed that can overcome the intrinsic limitations of Raman tags, and it was successfully applied to label-free living cell SERS datasets for classifying cancer subtypes and cellular drug responses. Furthermore, dual-recognition label-SERS with digital assay revealed improved accuracy in quantitative dopamine analysis. Advanced machine learning (artificial neural network) was exploited to improve the interpretability of SERS bioanalysis for multiple cellular drug responses. Finally, this dissertation provides future perspectives with different aspects, including SERS, biology, and statistics, for SERS to potentially become a standard analytical method that can compete with or complement existing technologies.

Optofluidic sensing utilizes the advantages of both microfluidic and optical science to achieve tunable and reconfigurable high-performance sensing purpose, which has established itself as a new and dynamic research field for exciting developments at the interface of photonics, microfluidics, and the life sciences. With the trend of developing miniaturized electronic devices and integrating multi-functional units on lab-on-a-chip instruments, more and more desires request for novel and powerful approaches to integrating optical elements and fluids on the same chip-scale system in recent years. By taking advantage of the electrowetting phenomenon, the wettability of liquid droplet on micro/nano-structured surfaces and the Leidenfrost effect, this doctoral research focuses on developing high-performance optofluidic sensing systems, including optical beam adaptive steering, whispering gallery mode (WGM) optical sensing, and surface-enhanced Raman spectroscopy (SERS) sensing. A watermill-like beam steering system is developed that can adaptively guide concentrating optical beam to targeted receivers. The system comprises a liquid droplet actuation mechanism based on electrowetting-on-dielectric, a superlattice-structured rotation hub, and an enhanced optical reflecting membrane. The specular reflector can be adaptively tuned within the lateral orientation of 360°, and the steering speed can reach ~353.5°/s. This work demonstrates the feasibility of driving a macro-size solid structure with liquid microdroplets, opening a new avenue for developing reconfigurable components such as optical switches in next-generation sensor network. Furthermore, the WGM sensing system is demonstrated to be stimulated along the meridian plane of a liquid microdroplet, instead of equatorial plane, resting on a properly designed nanostructured chip surface. The unavoidable deformation along the meridian rim of the sessile microdroplet can be controlled and regulated by tailoring the nanopillar structures and their associated hydrophobicity. The nanostructured superhydrophobic chip surface and its impact on the microdroplet morphology are modeled by Surface Evolver (SE), which is subsequently validated by the Cassie-Wenzel theory of wetting. The influence of the microdroplet morphology on the optical characteristics of WGMs is further numerically studied using the Finite-Difference Time-Domain method (FDTD) and it is found that meridian WGMs with intrinsic quality factor Q exceeding 104 can exist. Importantly, such meridian WGMs can be efficiently excited by a waveguiding structure embedded in the planar chip, which could significantly reduce the overall system complexity by eliminating conventional mechanical coupling parts. Our simulation results also demonstrate that this optofluidic resonator can achieve a sensitivity as high as 530 nm/RIU. This on-chip coupling scheme could pave the way for developing lab-on-a-chip resonators for high-resolution sensing of trace analytes in various applications ranging from chemical detections, biological reaction processes to environmental protection. Lastly, this research reports a new type of high-performance SERS substrate with nanolaminated plasmonic nanostructures patterned on a hierarchical micro/nanostructured surface, which demonstrates SERS enhancement factor as high as 1.8 x 107. Different from the current SERS substrates which heavily relies on durability-poor surface structure modifications and various chemical coatings on the platform surfaces which can deteriorate the SERS enhancement factor (EF) as the coating materials may block hot spots, the Leidenfrost effect-inspired evaporation approach is proposed to minimize the analyte deposition area and maximize the analyte concentration on the SERS sensing substrate. By intentionally regulating the temperature of the SERS substrate during evaporation process, the Rhodamine 6G (R6G) molecules inside a droplet with an initial concentration of 10-9 M is deposited within an area of 450 μm2, and can be successfully detected with a practical detection time of 0.1 s and a low excitation power of 1.3 mW. / Doctor of Philosophy / Over the past two decades, optofluidics has emerged and established itself as a new and exciting research field for novel sensing technique development at the intersection of photonics, microfluidics and the life sciences. The strong desire for developing miniaturized lab-on-a-chip devices and instruments has led to novel and powerful approaches to integrating optical elements and fluids on the same chip-scale systems. By taking advantage of the electrowetting phenomenon, the wettability of liquid droplet on micro/nano-structured surfaces and the Leidenfrost effect, this doctoral program focuses on developing high-performance optofluidic sensing systems, including optical beam adaptive steering, whispering gallery mode (WGM) optical sensing, and surface-enhanced Raman spectroscopy (SERS) sensing. During this doctoral program, a rotary electrowetting-on-dielectric (EWOD) beam steering system was first fabricated and developed with a wide lateral steering range of 360° and a fast steering speed of 353.5°/s, which can be applied in telecommunication systems or lidar systems. Next, the meridian WGM optical sensing system was optically simulated using finite difference time domain (FDTD) method and was numerically validated to achieve a high quality-factor Q exceeding 104 and a high refractive index sensitivity of 530 nm/RIU, which can be applied to the broad areas of liquid identification or single molecule detection. Lastly, a SERS sensing platform based on a hierarchical micro/nano-structured surface was accomplished to exhibit a decent SERS enhancement factor (EF) of 1.81 x 107. The contact angle of water droplet on the SERS substrate is 134° with contact angle hysteresis of ~32°. Therefore, by carefully controlling the SERS surface temperature, we employed Leidenfrost evaporation to concentrate the analytes within an extremely small region, enabling the high-resolution detection of analytes with an ultra-low concentration of ~10-9 M.

The work focused on addressing four main objectives. The first objective was to quantify protein and amino acid substitution reactions. Michael addition reactions were used to modify the amino acids and protein. Amino acids alanine, cysteine, and lysine, and protein ovalbumin (OA) were substituted with different concentrations of ethyl vinyl sulfone (EVS). The substituted products were analyzed using Raman spectroscopy and UV-spectroscopy based ninhydrin assay. In case of alanine, Raman and UV results correlated with each other. With cysteine at lower EVS substitutions amine on the main chain was the preferred site while the substitution shifted to thiols at higher substitutions. This could only be discerned using Raman spectroscopy. Lysine has amines on the main chain and side chain while main chain amine was the most reactive site at lower concentrations of EVS while at higher concentrations side chain amines were also substituted. This information could be discerned using Raman spectroscopy only and not UV spectroscopy. In case of protein as observed by Raman and UV spectroscopy the reaction continued at higher concentrations of EVS indicating the participation of glutamine and asparagines at higher substitutions. However, the reaction considerably slowed down at higher EVS substitutions. The second objective of the study was to decrease the glass transition temperature (Tg) of OA through internal plasticization and also study the effects of the substituents on the thermal stability of OA. The hypothesis was by covalently attaching substituents to OA, number of hydrogen bonds can be reduced while increasing the free volume and this would reduce Tg. EVS, acrylic acid (AA), butadiene sulfone (BS) and maleimide (MA) were the four groups used. EVS was the most efficient plasticizer of all the four substituents. The Tg decreased with the increasing concentration of EVS until all of the reactive of groups on OA were used up. Tg decreased slightly with AA and BS while no change was observed with MA. However, the substituents showed exact opposite trend in thermal stability as measured using thermogravimetric analysis (TGA). The thermal stability of MA substituted OA was the highest and that of EVS substituted OA was least. FT-IR spectroscopy results indicated that all four substituents caused structural changes in OA. This implied that there were intermolecular interactions between substituted protein chains in case of AA, BS, and MA. This caused an increase in the thermal stability. EVS on the other hand is a linear chain monomer with a hydrophobic end group and hence could not participate in the intermolecular interactions and hence caused a decrease in Tg. As mentioned above the limitation to this technique is the number of available reactive groups on the protein. However, we successfully demonstrated the feasibility of this method in decreasing Tg of protein. The third objective was to create hydrogels by crosslinking OA with divinyl sulfone (DVS). Protein hydrogels due to their biocompatible nature find applications in drug delivery and tissue engineering. For tissue engineering applications the hydrogels need to be mechanically stable. In this study the protein was substituted with EVS or AA and then crosslinked with DVS. The swelling ratio was measured as a function of pH. All the hydrogels showed the same trend and swelled the least at pH 4.5 which is the isoelectric point of the protein. At basic pH conditions EVS substituted hydrogels swelled the most while AA substituted hydrogels showed least swelling. The static and dynamic moduli of the hydrogels were determined using tensile tester and rheometer respectively. The static modulus values were three times the dynamic modulus. The modulus of the control which is crosslinked OA was least and that of AA substituted OA was highest. The stress relaxation test also showed similar results in which AA substituted OA relaxed the most and the control relaxed the least. FT-IR of the dry hydrogels showed that the amount of hydrogen bonding increased with AA substitution. The hydrophilic AA end groups interacted with each other forming hydrogen bonds. These hydrogen bonds served as additional crosslinks there by increasing the modulus of the hydrogels. EVS on the other hand was incapable of interactions due to the lack of hydrophilic end groups. We were successfully able to create protein hydrogels and control the swelling and mechanical properties by varying the amount of substituted group. The final objective of the study was to create and characterize microstructures from substituted alanine and lysine. Alanine and lysine were substituted with different concentrations of EVS. Bars and fibers were observed for alanine at moderate substitutions while at higher concentrations random structures were observed using scanning electron microscopy (SEM). Lysine formed tubes at moderate EVS substitutions and rosettes at high concentrations of EVS as evidenced by SEM. FT-IR results suggested that instead of carbonyl one of sulfonyl bonded to the available amine in modified amino acids. And only in this case fibers, tubes and rosettes were observed. X-ray diffraction (XRD) results supported this observation. Using these results we hypothesized that the self assembled structures very much depended on the amount of EVS present in the substituted product and sulfonyl forming β-sheet analogs with amine. / Ph. D.

Engineering tools at the nano-bio interface have enabled transformative advances in molecular diagnostics, therapeutic monitoring, and cellular manipulation. However, challenges remain in achieving continuous real-time sensing, intracellular probing, and controlled actuation within an integrated, multifunctional platform. Nanotechnology, particularly through localized surface plasmons (LSPs), addresses these challenges by leveraging radiative decay for enhanced optical sensing (e.g., SERS) and non-radiative decay for nanoscale actuation (e.g., photothermal effects and vapor nanobubbles). Conventional plasmonic systems, however, are limited in wavelength multiplexing, versatility, and spatial mode overlap. To overcome these shortcomings, this dissertation presents a wavelength-multiplexed multimodal optical nano-bio interfaces enabled by multiresonant plasmonic architectures. These systems combine advanced plasmonic designs with intimate bio-nano interfaces, achieving multifunctionality across a broad spectral range for biochemical sensing and nanoscale actuation. The core platform is built on metal-insulator-metal (MIM) plasmonic nanolaminate nanopillar arrays (NLNPAs), which provide tunable multiresonant responses, nanoscale mode overlap, and an intimate bio-nano interface. For biochemical sensing, the multiband plasmonic resonances enable broadband surface-enhanced Raman scattering (SERS), offering high sensitivity and molecular specificity across a wide spectral range. This capability facilitates high-dimensional molecular fingerprinting, providing insights into spatial-temporal biochemical processes. Additionally, the platform enhances nonlinear optical processes, such as second- and third-harmonic generation (SHG/THG), enabling broadband, label-free sensing and bio-actuation with tunable performance. Beyond sensing, the multiresonant plasmonic interface supports precise nanoscale actuation through femtosecond laser-induced vapor nanobubbles. This approach enables highly localized, minimally invasive membrane permeabilization—optoporation—facilitating intracellular biochemical sensing and molecular delivery with nanoscale precision. Such capabilities hold significant promise for applications in bio-nanophotonics, targeted drug delivery, and cellular biochemical analysis, offering a pathway for advancing molecular diagnostics, minimally invasive therapies, and precise nanosurgery. As a proof-of-concept, a vapor nanobubble-enabled regenerative SERS sensing platform is demonstrated for continuous, wavelength-multiplexed biochemical monitoring. By combining photothermal nanocavitation with plasmonic SERS hotspots, the system achieves ultrasensitive molecular detection in protein-rich biofluids, such as bacterial biofilms associated with chronic wounds. This platform allows real-time monitoring of biochemical evolution in complex biointerfaces, offering a robust tool for continuous molecular fingerprinting in dynamic biological systems. Collectively, these advancements establish the wavelength-multiplexed multimodal optical nano-bio interface as a versatile platform that bridges the gap between nanoscale optical engineering and biological applications. By enabling simultaneous spatial-temporal sensing and actuation with nanoscale precision, this work paves the way for transformative applications in molecular diagnostics, real-time therapeutic monitoring, and cellular biochemical analysis. Future efforts toward portable instrumentation and integration with wearable or implantable technologies will further enhance the platform's potential for non-invasive, real-time monitoring in clinical and healthcare settings, driving forward the future of bio-nanophotonics. / Doctor of Philosophy / The ability to observe, analyze, and control biological processes at the tiniest scales—down to individual cells and molecules— has the potential to transform our understanding of life and revolutionize medicine, diagnostics, and healthcare. Imagine tools that can simultaneously detect disease-related molecules, deliver medicine with pinpoint accuracy, and monitor changes happening inside cells in real time. Achieving this, however, is no small feat. Existing tools often lack the ability to perform multiple tasks at once or adapt to the dynamic nature of living systems. To address this, we developed a new type of nano-bio interface that uses specialized nanostructures to interact with light in unique ways. These tiny structures can trap and amplify light across a wide range of colors, allowing us to achieve multifunctional capabilities at different colors: detecting molecules, probing inside cells, and even triggering specific biological responses using short bursts of laser light. For sensing, the system enhances Raman spectroscopy, a technique that reads the molecular "fingerprints" of chemicals, helping us detect and identify molecules with high precision. For cellular manipulation, we use short laser pulses to generate tiny bubbles that can temporarily open cell membranes—optoporation—enabling drug delivery or accessing the cell's biochemical content without causing harm. Additionally, the system can monitor changes over time, such as the molecular activity within bacterial biofilms, which are responsible for chronic infections. This work opens exciting new possibilities for medicine and biology: detecting diseases earlier, delivering therapies more precisely, and analyzing biological processes in real time. In the future, these nano-tools could be incorporated into portable devices, wearables, or implants, enabling doctors and scientists to monitor health and treat diseases in ways that are faster, safer, and more effective.

When these fluids interact with the surrounding rocks, small aliquots of these fluids are trapped as imperfections in the crystal lattice and fractures of minerals. These microscopic features are called fluid and melt inclusions, and are one of the best tools available to probe, measure and determine the chemical and physical properties of crustal fluids. In the present study we examine new developments into our understanding of fluid-rock interactions using fluid and melt inclusion as tools to provide insights into the evolution of the Earth's crust from the deep continental crust to the surface. Chapter II "Raman spectroscopic characterization of H2O in CO2-rich fluid inclusions in granulite facies metamorphic rocks", is a brief review of the current understanding of granulite rocks and their formation, and a new development into our ability to characterize the composition of the fluids trapped as fluid inclusions in minerals in granulite facies rocks. Chapter III "Reassessment of the Raman CO2 densimeter", details new developments in the use of the Raman spectroscopy to characterize the density of CO2. In this chapter we describe briefly the Raman effect of CO2 and the density dependence of the Fermi diad using different Raman instruments, laser sources and gratings to understand the differences in the published data. Chapter IV "Serpentinization reaction rates measured in olivine micro-batch reactors" describes new insights into the serpentinization process by using olivine micro-reactors. The micro-reactor technique is a new experimental development that allows researchers to monitor the fluid chemistry as well as the mineral composition changes inside synthetic fluid inclusion. / Ph. D.

Combinatorial approaches in metabolic engineering can make use of randomized mutations and/or overexpression of randomized DNA fragments. When DNA fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a novel, efficient, and reproducible technique for creating DNA libraries was created in this research based on whole genome amplification using degenerate oligonucleotide primed PCR (DOP-PCR). The approach can produce DNA libraries from nanograms of a template genome or the metagenome of multiple microbial populations. The DOP-PCR primers contain random bases, and thermodynamics of hairpin formation was used to design primers capable of binding randomly to template DNA for amplification with minimal bias. Next-generation high-throughput sequencing was used to determine the design is capable of amplifying up to 98% of template genomic DNA and consistently out-performed other DOP-PCR primers. Application of these new DOP-PCR amplified DNA libraries was demonstrated in multiple strain enrichments to isolate genetic library fragments capable of (i) increasing tolerance of E. coli ER2256 to toxic levels of 1-butanol by doubling the growth rate of the culture, (ii) redirecting metabolism to ethanol and pyruvate production (over 250% increase in yield) in Clostridium cellulolyticum when consuming cellobiose, and (iii) enhancing L-arginine production when used in conjunction with a new synthetic gene circuit. / Ph. D.

Individual carbon nanotubes have been theoretically and experimentally proven to be the strongest and stiffest materials discovered to date with tensile strengths ranging from 1-5 TPa and elastic modulus values as high as 150 GPa. In this work, the recent development of continuous sheets of CNTs, produced by Nanocomp Technologies Inc ., are investigated for their potential as reinforcement in polymer matrix composite (PMC) materials. The potential of these nanotube-based PMC materials have been reported by researchers at Florida State University (FSU). Through the use of mechanical stretching procedures to increase the alignment of the nanotubes within the CNT sheets, the tensile strength and Young's modulus of the composites in the FSU study averaged 3081 MPa and 350 GPa, respectively. These values are for composites fabricated from 40% stretched CNT sheets and are 48% and 107% improvements over composites fabricated from the pristine, unstretched CNT sheets. However, the test specimens used in the FSU study consisted of a single CNT ply and each coupon was individually stretched and cured for testing. Therefore, the process used to generate the coupons which exhibited these high mechanical properties would be difficult to scale to a usable size for aerospace structural components. In the current study, a scalable process has been developed in which 2-ply, 3" x 3" panels of CNT and resin composites are fabricated. An apparatus and methodology for mechanically stretching the CNT sheets used in these composite panels has also been developed. After initial testing was conducted with the CNT composites and the coupons exhibited significant elongation at failure, along with the absence of a linear elastic region, conventional test standards for material testing were deemed impractical. For this reason, new mechanical testing methodologies have been developed to determine the mechanical properties of specific strength and specific modulus of CNT-polymer composites. In order to obtain the maximum benefits of a fiber in any matrix in terms of stiffness and strength, it is preferable to align the high strength and stiffness fibers in the direction of loading. Given that these CNT sheets essentially consist of billions of short, discontinuous CNTs of 2-3mmin length, the process of mechanical stretching is used in an attempt to align these tubes in the direction of the applied tensile load. Here we have explored methodologies for stretching, fabricating, and mechanical testing. Having identified a process which seems viable, an examination into the effect of the mechanical stretching to increase the alignment of the nanotubes within the CNT sheets, and thus to increase the material properties of the 2-ply composites constructed from them, is conducted. In order to correlate the enhancements in the mechanical properties with the increased alignment of the CNTs, polarized Raman spectroscopy techniques have been used. Lastly, Scanning Electron Microscopy (SEM) is used to examine the effect of stretching on the pristine CNT sheet, as well as examine the fracture surfaces of failed test coupons to better characterize the failure modes. In this report, polarized Raman spectroscopy has been used to confirm the enhancedalignment of nanotubes within the CNT sheets through the used of a nematic order parameter. Unstretched sheets exhibit an order parameter of 0.07 and 0.09 for untreated and Acetone treated sheets, respectively. Upon stretching the untreated sheets to 45%, the order parameter increases to 0.1409 and, when stretched to 30%, Acetone treated sheets have an order parameter of 0.1518. During the mechanical testing of 2-ply composites fabricated from stretched CNT sheets, the effect of this increased alignment is made apparent. Untreated CNT sheets are used to fabricate 2-ply composites after being stretched and are compared to baseline values of panels fabricated using sheets which are not stretched. In the panels fabricated with PEI resin and 43% stretched, untreated CNT sheets, a 137% increase in average specific strength and a 44% increase in average specific modulus over the baseline panel is observed. For panels fabricated with BMI and 33% stretched, untreated CNT sheets, a 169% increase in average specific strength and 105% increase in average specific modulus is observed when compared to the baseline panel. These increases are evidence for the potential of mechanical stretching to align the nanotubes within the CNT sheets and bolster the mechanical properties of resulting CNT-polymer composites. / Master of Science