Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.

<p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>M-DNA is a novel complex formed between DNA and transition metal ions under alkaline conditions.<span style='mso-spacerun:yes'>  </span>The unique properties of M-DNA were manipulated in order to rationally place metal ions at specific regions within a double-stranded DNA helix.<span style='mso-spacerun:yes'>   </span>Investigations using thermal denaturation profiles and the ethidium fluorescence assay illustrate that the pH at which M-DNA formation occurs is influenced heavily by the DNA sequence and base composition.<span style='mso-spacerun:yes'>  </span>For instance, DNA with a sequence consisting of poly[d(TG)d(CA)] is completely converted to M-DNA at pH 7.9 while DNA consisting entirely of poly[d(AT)] remains in the B-DNA conformation until a pH of 8.6 is reached.<span style='mso-spacerun:yes'>  </span>The pH at which M-DNA formation occurs is further decreased by the incorporation of 4-thiothymine (s⁴T).<span style='mso-spacerun:yes'>  </span>DNA oligomers with a mixed sequence composed of </span>half d(AT) and the other half d(TG)d(CA)<span style='mso-bidi-font-weight: bold'> showed that only 50% of the DNA is able to incorporate Zn²⁺ ions at pH 7.9.<span style='mso-spacerun:yes'>  </span>This suggests that only regions corresponding to the tracts of <span class=GramE>d(</span>TG)d(CA) are being transformed.<span style='mso-spacerun:yes'>   </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-fareast-language:ZH-CN'>Duplex DNA monolayers were self-assembled on gold through <span class=GramE>a</span> Au-S linkage and both B- and M-DNA conformations were studied using X-ray photoelectron spectroscopy (XPS) in order to better elucidate the location of the metal ions.<span style='mso-spacerun:yes'>  </span>The film thickness, density, elemental composition and ratios for samples were analyzed and compared.<span style='mso-spacerun:yes'>  </span>The DNA surface coverage, calculated from both XPS and electrochemical measurements, was <span class=GramE>approximately 1.2 x 10¹³molecules/cm²</span>for B-DNA.<span style='mso-spacerun:yes'>  </span>All samples showed distinct peaks for C 1s, O 1s, N 1s, P 2p and S 2p as expected for a thiol-linked DNA.<span style='mso-spacerun:yes'>  </span></span><span style='mso-bidi-font-weight: bold'>On addition of Zn²⁺ to form M-DNA the C 1s, P 2p and S 2p showed only small changes </span><span style='mso-fareast-language:ZH-CN'>while both the N 1s and O 1s spectra changed considerably.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ interacting with oxygen on the phosphate backbone as well as replacing the imino protons of thymine (T) and guanine (G) in M-DNA.<span style='mso-spacerun:yes'>   </span>Analysis of the Zn 2p spectra also demonstrated that the concentration of Zn²⁺ present under M-DNA conditions is consistent with Zn²⁺ binding to both the phosphate backbone as well as replacing the imino protons of T or G in each base pair.<span style='mso-spacerun:yes'>  </span>After the M-DNA monolayer is washed with a buffer containing only Na⁺ the Zn²⁺ bound to the phosphate backbone is removed while the Zn²⁺ bound internally still remains. </span><span style='mso-bidi-font-weight:bold'>Variable angle x-ray photoelectron spectroscopy (VAXPS) was also used to examine monolayers consisting of mixed sequence oligomers.<span style='mso-spacerun:yes'>  </span>Preliminary results suggest that under M-DNA conditions, the zinc to phosphate ratio changes relative to the position of the <span class=GramE>d(</span>TG)d(CA) tract being at the top or bottom of the monolayer.<span style='mso-spacerun:yes'>  </span><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>Electrochemistry was also used to investigate the properties of M-DNA monolayers on gold and examine how the localization of metal ions affects the resistance through the DNA monolayer.<span style='mso-spacerun:yes'>  </span>T</span>he effectiveness of using the IrCl₆^2-/3-redox couple to investigate DNA monolayers and the potential advantages of this system over the standard Fe(CN)₆^3-/4- redox couple are demonstrated.<span style='mso-spacerun:yes'>  </span>B-DNA monolayers were converted to M-DNA by incubation in buffer containing 0.4 mM Zn²⁺ at pH 8.6 and studied by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA) with IrCl₆^2-/3-.<span style='mso-spacerun:yes'>  </span>^{<span style='mso-spacerun:yes'> </span>}Compared to B-DNA, M-DNA showed significant changes in CV, EIS and CA spectra.<span style='mso-spacerun:yes'>  </span>However, only small changes were observed when the monolayers were incubated in Mg²⁺at pH 8.6 or in Zn²⁺ at pH 6.0.<span style='mso-spacerun:yes'>  </span>The heterogeneous electron-transfer rate (<i style='mso-bidi-font-style:normal'>k</i>_ET) between the redox probe and the surface of a bare gold electrode was determined to be 5.7 x 10^-3 cm/s.<span style='mso-spacerun:yes'>  </span>For a B-DNA modified electrode, the <i style='mso-bidi-font-style:normal'>k</i>_ET through the monolayer was too slow to be measured.<span style='mso-spacerun:yes'>  </span>However, under M-DNA conditions, a <i style='mso-bidi-font-style:normal'>k</i>_ET of 1.5 x 10^-3 cm/s was reached.<span style='mso-spacerun:yes'>  </span>As well, the percent change in resistance to charge transfer (R_CT), measured by EIS, <span class=GramE>was</span> used to illustrate the dependence of M-DNA formation on pH.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ ions replacing the imino protons on thymine and guanine residues.<span style='mso-spacerun:yes'>  </span>Also, at low pH values, the percent change in R_CT seems to be greater for <span class=GramE><span style='mso-bidi-font-weight:bold'>d(</span></span><span style='mso-bidi-font-weight: bold'>TG)₁₅d(CA)₁₅ compared to oligomers with mixed d(AT) and d(TG)d(CA) tracts.<span style='mso-spacerun:yes'>  </span></span>The IrCl₆^2-/3-redox couple was also effective in differentiating between single-stranded and double-stranded DNA during dehybridization and rehybridization experiments.<span style='mso-spacerun:yes'>  </span><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>

Detection of conformational and structural shifts in biomolecules is of great importance in bioanalytical chemistry and pharmaceutical sciences. Transverse shear mode acoustic wave devices have been used as real-time, label-free detectors of conformational shifts in biomolecules on surfaces. However, material changes in the biochemical monolayer and coupling between the substrate and the surrounding liquid make it difficult to isolate the desired signal, so an understanding of these phenomena is required. In this thesis, interfacial slip, viscoelasticity, and structural changes are used to model acoustic signals due to surface adsorption of the protein neutravidin, immobilisation of HIV-1 TAR RNA, and subsequent interaction of the RNA with tat peptide fragments. Binding of tat peptides induces conformational changes in the TAR. Similar modelling is performed to describe experiments involving the binding of calcium to surface-attached calmodulin, which is also known to result in a conformational shift. The aim of the modelling is to isolate the sensor response due to conformational shifts. The biomolecules are described as hydrated, viscoelastic monolayers and slip is allowed at all interfaces. All models are numerically fit to experimental values using a two-parameter minimisation algorithm. Slip is found on the electrode surface prior to neutravidin adsorption. Neutravidin and TAR are described as distinct viscoelastic monolayers. Binding of tat peptide fragment to the TAR monolayer is modelled using a complex slip parameter and a change in length, corresponding to a straightening of the molecule. Similarly, numerical modelling of calmodulin results reveals a length change in the molecule upon calcium binding. Molecular dynamics (MD) simulations of the TAR-tat fragment system are performed to corroborate the modelling results. Starting structures are computed by molecular docking, and MD simulations of TAR complexed with various length tat fragments are described. The simulations are in general agreement with the modelling results and literature values from similar molecular dynamics experiment. A new parameter is introduced to describe biomolecule-solvent affinity, and is compared to interfacial coupling values obtained from modelling. This research demonstrates that acoustic wave devices can be used to detect conformational shifts in surface-attached biomolecules, provided molecular details about the shifts are known.

Nanophotonics, especially plasmonics is a kind of very active research area, which deals with the interaction behavior between electromagnetic radiation and metallic nanostructures. It has attracted enormous attention over recent decades due to its great potential of ripple effects on electronics, energy, environmental, and medical industries as well as scientific interests. In particular, noble metal nanoparticles exhibit localized surface plasmon resonance (LSPR), which is the collective oscillating excitation of the free electrons on the surface of metal nanoparticles when light is incident on the particle. The LSPR extinction peak is very sensitive to the dielectric environment near the particle surface and can be tailored by the particle's sizes and shapes. These properties allow LSPR-active substrate using plasmonic gold nanoparticles to be a great transducer for biosensing with real-time and label-free measurement. In addition, the plasmonic gold nanoparticles such as gold nanorod and bipyramid are prepared by the seed-mediated and surfactant-directed method based on the cetyltrimethylammonium bromide (CTAB), which has a great influence on the synthesis. In the growth mechanism, it is believed that CTAB interacts with different facet and defects on the growing nanoparticles to produce different rate of gold ion reduction onto the nanoparticles to generate anisotropic growth. Therefore, CTAB layer is greatly interesting because the modification of nanoparticles surface chemistry is essential to biological targeting, film formation, and assembly of complex structures. Surface enhanced Raman spectroscopy (SERS) of gold nanorods in CTAB solution has been used to analyze a surfactant structural transition based on the distance dependent electromagnetic enhancement. As the surfactant concentration in the gold nanorod solution was reduced, a structural transition in the surfactant layer between 2 mM and 5 mM CTAB solution was observed through a sudden increase in the signal from the alkane chains. A structural transition in the CTAB layer that stabilizes gold nanorods was identified by comparing the intensities of different bands within the CTAB molecule. Therefore, the surface manipulation and analysis of the nanostructures and their interface with controlled environment provide important insight into their structural function and interpretation, and many opportunities for biomedical applications.

<p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>M-DNA is a novel complex formed between DNA and transition metal ions under alkaline conditions.<span style='mso-spacerun:yes'>  </span>The unique properties of M-DNA were manipulated in order to rationally place metal ions at specific regions within a double-stranded DNA helix.<span style='mso-spacerun:yes'>   </span>Investigations using thermal denaturation profiles and the ethidium fluorescence assay illustrate that the pH at which M-DNA formation occurs is influenced heavily by the DNA sequence and base composition.<span style='mso-spacerun:yes'>  </span>For instance, DNA with a sequence consisting of poly[d(TG)d(CA)] is completely converted to M-DNA at pH 7.9 while DNA consisting entirely of poly[d(AT)] remains in the B-DNA conformation until a pH of 8.6 is reached.<span style='mso-spacerun:yes'>  </span>The pH at which M-DNA formation occurs is further decreased by the incorporation of 4-thiothymine (s⁴T).<span style='mso-spacerun:yes'>  </span>DNA oligomers with a mixed sequence composed of </span>half d(AT) and the other half d(TG)d(CA)<span style='mso-bidi-font-weight: bold'> showed that only 50% of the DNA is able to incorporate Zn²⁺ ions at pH 7.9.<span style='mso-spacerun:yes'>  </span>This suggests that only regions corresponding to the tracts of <span class=GramE>d(</span>TG)d(CA) are being transformed.<span style='mso-spacerun:yes'>   </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-fareast-language:ZH-CN'>Duplex DNA monolayers were self-assembled on gold through <span class=GramE>a</span> Au-S linkage and both B- and M-DNA conformations were studied using X-ray photoelectron spectroscopy (XPS) in order to better elucidate the location of the metal ions.<span style='mso-spacerun:yes'>  </span>The film thickness, density, elemental composition and ratios for samples were analyzed and compared.<span style='mso-spacerun:yes'>  </span>The DNA surface coverage, calculated from both XPS and electrochemical measurements, was <span class=GramE>approximately 1.2 x 10¹³molecules/cm²</span>for B-DNA.<span style='mso-spacerun:yes'>  </span>All samples showed distinct peaks for C 1s, O 1s, N 1s, P 2p and S 2p as expected for a thiol-linked DNA.<span style='mso-spacerun:yes'>  </span></span><span style='mso-bidi-font-weight: bold'>On addition of Zn²⁺ to form M-DNA the C 1s, P 2p and S 2p showed only small changes </span><span style='mso-fareast-language:ZH-CN'>while both the N 1s and O 1s spectra changed considerably.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ interacting with oxygen on the phosphate backbone as well as replacing the imino protons of thymine (T) and guanine (G) in M-DNA.<span style='mso-spacerun:yes'>   </span>Analysis of the Zn 2p spectra also demonstrated that the concentration of Zn²⁺ present under M-DNA conditions is consistent with Zn²⁺ binding to both the phosphate backbone as well as replacing the imino protons of T or G in each base pair.<span style='mso-spacerun:yes'>  </span>After the M-DNA monolayer is washed with a buffer containing only Na⁺ the Zn²⁺ bound to the phosphate backbone is removed while the Zn²⁺ bound internally still remains. </span><span style='mso-bidi-font-weight:bold'>Variable angle x-ray photoelectron spectroscopy (VAXPS) was also used to examine monolayers consisting of mixed sequence oligomers.<span style='mso-spacerun:yes'>  </span>Preliminary results suggest that under M-DNA conditions, the zinc to phosphate ratio changes relative to the position of the <span class=GramE>d(</span>TG)d(CA) tract being at the top or bottom of the monolayer.<span style='mso-spacerun:yes'>  </span><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>Electrochemistry was also used to investigate the properties of M-DNA monolayers on gold and examine how the localization of metal ions affects the resistance through the DNA monolayer.<span style='mso-spacerun:yes'>  </span>T</span>he effectiveness of using the IrCl₆^2-/3-redox couple to investigate DNA monolayers and the potential advantages of this system over the standard Fe(CN)₆^3-/4- redox couple are demonstrated.<span style='mso-spacerun:yes'>  </span>B-DNA monolayers were converted to M-DNA by incubation in buffer containing 0.4 mM Zn²⁺ at pH 8.6 and studied by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA) with IrCl₆^2-/3-.<span style='mso-spacerun:yes'>  </span>^{<span style='mso-spacerun:yes'> </span>}Compared to B-DNA, M-DNA showed significant changes in CV, EIS and CA spectra.<span style='mso-spacerun:yes'>  </span>However, only small changes were observed when the monolayers were incubated in Mg²⁺at pH 8.6 or in Zn²⁺ at pH 6.0.<span style='mso-spacerun:yes'>  </span>The heterogeneous electron-transfer rate (<i style='mso-bidi-font-style:normal'>k</i>_ET) between the redox probe and the surface of a bare gold electrode was determined to be 5.7 x 10^-3 cm/s.<span style='mso-spacerun:yes'>  </span>For a B-DNA modified electrode, the <i style='mso-bidi-font-style:normal'>k</i>_ET through the monolayer was too slow to be measured.<span style='mso-spacerun:yes'>  </span>However, under M-DNA conditions, a <i style='mso-bidi-font-style:normal'>k</i>_ET of 1.5 x 10^-3 cm/s was reached.<span style='mso-spacerun:yes'>  </span>As well, the percent change in resistance to charge transfer (R_CT), measured by EIS, <span class=GramE>was</span> used to illustrate the dependence of M-DNA formation on pH.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ ions replacing the imino protons on thymine and guanine residues.<span style='mso-spacerun:yes'>  </span>Also, at low pH values, the percent change in R_CT seems to be greater for <span class=GramE><span style='mso-bidi-font-weight:bold'>d(</span></span><span style='mso-bidi-font-weight: bold'>TG)₁₅d(CA)₁₅ compared to oligomers with mixed d(AT) and d(TG)d(CA) tracts.<span style='mso-spacerun:yes'>  </span></span>The IrCl₆^2-/3-redox couple was also effective in differentiating between single-stranded and double-stranded DNA during dehybridization and rehybridization experiments.<span style='mso-spacerun:yes'>  </span><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>

The syntheses of novel poly(paraphenyleneethynylene)s, PPEs, and poly(aryleneeethynylene)s, PAEs, as well as hybrid poly(paraphenyleneethynylene)- poly(paraphenylenevinylene)s, PPE-PPVs, are presented. Fluorescent PPEs decorated with biologically relevant ligands are utilized in model biosensing schemes. PPE-PPV hybrids, as well as their highly emissive oligomeric, cruciform model compounds are studied in an effort to modify the bandgap of the parent PPE backbone. Improved hole and electron injection capabilities are demonstrated with these hybrid conjugated materials. Structural variation and morphological effects of PPEs, PPE-PPVs and model compounds are studied to elucidate the effects upon the photophysical properties of the emissive materials.

The Microelectronics Group has been researching sensors useful for detecting and quantifying events in biological molecular chemistry, for example, binding events. Our previous research has been based primarily on quartz resonators. This thesis describes the results of our initial research of Surface Plasmon Resonance (SPR) based technology. This study contains the design and implementation of a fully functional SPR biosensor with detailed disclosure of monolayer construction, digital hardware interfaces and software algorithms for process the SPR sensors output. An antibody monolayer was constructed on the biosensor surface with the goal of setting the strengths, weaknesses and limitation of measuring molecular events with SPR technology. We documented several characteristics of molecular chemistry that directly effect any measurements made using Surface Plasmon Resonance technology including pH, free ions, viscosity and temperature. Furthermore, the component used in our study introduced additional limitations due to wide variations amongst parts, the constraint of a liquid medium and the large surface area used for molecular interrogation. We have identified viable applications for this sensor by either eliminating or compensating for the factors that affect the measured results. This research has been published at the inaugural IEEE sensors conference and to our knowledge is the first time a biosensor has been constructed by attaching a sensor to a PDA and performing all signal processing, waveform analysis and display in the PDAs core processor.

Luminescent microspheres encapsulating glucose oxidase and an oxygensensitive lumophore have recently been reported as potential implantable sensors for in vivo glucose monitoring. However, there are two main issues that must be addressed for enzymatic systems such as these to realize the goal of minimally-invasive glucose monitoring. The first issue is related to the short response range of such sensors, less than 200 mg/dL, which must be extended to cover the full physiological range (0-600 mg/dL) of glucose possible for diabetics. The second issue is concerning the short operating lifetime of these systems due to enzyme degradation (less than 7 days). Two approaches were considered for increasing the range of the sensor response; nanofilm coatings and particle porosity. In the first approach, microparticle sensors were coated with layer-by-layer deposited thin nanofilms to increase the response range. It was observed that, a precise control on the response range of such sensors can be achieved by manipulating different characteristics (e.g., thickness, deposition condition, and the outermost capping layer) of the nanofilms. However, even with 15 bilayers of poly(allylamine hydrochloride)/poly(styrene sulfonate) (PAH/PSS) nanofilm, limited range was achieved (less than 200 mg/dL). By performing extrapolation on the data obtained for the experimentally-determined response range versus the number of PAH/PSS bilayers, it was predicted that a nanofilm coating comprising of more than 60 PAH/PSS bilayers will be needed to achieve a linear response up to 600 mg/dL. Using modeling, it was realized that a more effective method for achieving a linear response up to 600 mg/dL is to employ microparticles with higher porosity. Sensors were prepared from highly porous silica microparticles (diameter = 7 mu m, porosity = 0.6) and their experimental response was determined. Not surprisingly, the experimentally determined response range of such sensors was found to be higher than 600 mg/dL. To improve the longevity of these sensors, two approaches were employed; incorporation of catalase and increasing the loading of glucose oxidase. Catalase was incorporated into microparticles, which protects the enzyme from peroxide-mediated deactivation, and thus improves the stability of such sensors. Sensors incorporating catalase were found to ~5 times more stable than the GOx-only sensors. It was theoretically predicted, that by maximizing the loading of glucose oxidase within the microparticles, the longevity of such sensors can be substantially improved. Based on this understanding, sensors were fabricated using highly porous microparticles; response range did not vary even after one month of continuous operation under normal physiological conditions. Modeling predicts that 1 mM of glucose oxidase and 1 mM of catalase would extend the operating lifetime to more than 90 days.

A few computational models currently exist to predict heat production and dissipation in tissue when a tumor containing optically-tunable gold nanoparticles such as nanoshells or nanorods is illuminated with near infrared (NIR) laser. The validity of any computational model still needs to be established by experiments before its wide use for various future clinical applications. One of the possible ways to validate the model is through the heat measurements within a phantom made with tissue-equivalent heat-sensitive gel. Currently, there are a few recipes available for this type of gel and the majority of them use severely toxic ingredients. However, none of them seems to perfectly serve the current purposes. Therefore, the primary goal of this thesis work was to develop and characterize two new types of heat-sensitive gels, using relatively non-toxic substances for the in-phantom validation of computational models. Specifically, two novel agar based phantoms, TG1 and TG2, were developed and characterized. The basic optical response of these phantoms at 808 nm NIR light was determined to test their equivalency to human tissue. Thermal damage to the phantoms was quantified by heating them to specific temperatures and obtaining calibration curves to relate temperature and R2 relaxation rates. The phantoms were scanned with magnetic resonance imaging (MRI) to obtain T2 values. TG1 gel, agar and bovine serum albumin (BSA) mixture, was found not to be optically tissue-equivalent. However, TG1 gel demonstrated unambiguous digital response capable of distinguishing temperature of at least 70 °C compared to the sample receiving no heat. Additionally, TG1 gel produced high degree of linearity in the thermal therapy temperature regime (60 - 80 °C). TG2 gel containing agar mixed with BSA and Intralipid has exhibited tissue equivalency based on laser transmission measurements. TG2 gel exhibited heat damage based on T2 values, only when the temperature reaches 80 °C. This digital response is considered less sensitive in view of the fact that BSA starts to undergo denaturing and cause optical density change at approximately 70 °C. Both gels, however, have shown to be thermally stable at temperatures up to 80 °C with no evidence of gel melting being observed.

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