Two experiments explore the application of plasmonic nanoparticles to cellular pathology. The first devised a platform by which gold-silver nanoparticles act as differentiable labels for cell surface receptors under dark field imaging. By conjugating particles of various constitutions with receptor-targeting antibodies, particles scatter characteristically according to their plasmon peak. The second experiment programmed receptor placement via the patterning of two substrates and used the binding of SERS nanoparticles to explore the quantification of such targets at high-density. On one substrate, anchor pairs established receptors at specified distances in order to define the relationship between scattering intensity and the distance between SERS particles. On the second, anchor regions are filled with increasing densities of receptors and the particle-saturated substrates are probed to relate scattering intensity to particle density. This should discover the density-threshold between linear and non-linear scattering and inform the quantification of particles in the exponential density regime.

Glancing angle laser induced fluorescence was used to monitor the kinetics of the photodegradation of chlorophyll at the surface of various salt solutions. The loss was measured using varying wavelengths of actinic radiation in the presence and absence of gas phase ozone. The loss rate of illuminated chlorophyll was faster on salt water surfaces than fresh water surfaces, both in the presence and absence of ozone. On salt water surfaces, the dependence of the loss rate on [O3(g)] was different under illuminated conditions than in the dark. This was further investigated by measuring the excitation spectra and the dependence of chlorophyll loss on the concentration of salts at the salt water surface. The possible production of reactive halogen atoms is the likely reason for the observed enhancement. The following results provide evidence of photosensitized oxidation of halogen anions, in the UV-visible range of the spectrum, resulting in halogen atom release.

Understanding energy transfer at the molecular scale is both essential for the design of novel molecular level devices and vital for uncovering the fundamental properties of non-equilibrium open quantum systems. In this thesis, we first establish the connection between molecular scale devices -- molecular electronics and phononics -- and open quantum system models. We then develop theoretical tools to study various properties of these models. We extend the standard master equation method to calculate the steady state thermal current and conductance coefficients. We then study the scaling laws of the thermal current with molecular chain size and energy, and apply this tool to investigate the onset of nonlinear thermal current - temperature characteristics, thermal rectification and negative differential conductance. Our master equation technique is valid in the ``on-resonance" regime, referring to the situation in which bath modes in resonance with the subsystem modes are thermally populated. In the opposite ``off-resonance" limit, we develop the Energy Transfer Born-Oppenheimer method to obtain the thermal current scaling without the need to solve for the subsystem dynamics. Finally, we develop a mapping scheme that allows the dynamics of a class of open quantum systems containing coupled subsystems to be treated by considering the separate dynamics in different subsections of the Hilbert space. We combine this mapping scheme with path integral numerical simulations to explore the rich phenomenon of entanglement dynamics within a dissipative two-qubit model. The formalisms developed in this thesis could be applied for the study of energy transfer in different realizations, including molecular electronic junctions, donor-acceptor molecules, artificial solid state qubits and cold-atom lattices.

Although the air-ice interface is atmospherically important, it is difficult to model accurately because exclusion and precipitation of solutes during freezing, deposition of atmospheric species, and heterogeneous/photochemical processes all affect its properties. In this thesis, glancing-angle spectroscopic methods were developed to study ice surfaces. Glancing-angle Raman spectroscopy showed that nitrate is not strongly excluded to the ice surface during freezing, in contradiction with expectations based on equilibrium thermodynamics. Glancing-angle laser-induced fluorescence showed that hydronium ions are not strongly excluded when dilute acidic solutions (HNO3 or HCl) are frozen. These results suggest that solutes are not universally excluded and that care should be taken in modelling surface concentrations on ice. Deposition of HCl(g) was found to result in different pH responses at the "pure" vs. "salty" ice surfaces. Changes at the "salty" ice surface were consistent with the existence of a brine layer at the air-ice interface while changes at the "pure" ice surface were distinctly different, indicating that it may not be appropriate to model it as a cold, liquid layer. Significantly, results also suggest that the sea ice surface is buffered against pH changes, with important implications for interpreting pH-dependent chemistry. The conversion of sea-salt derived halides to reactive halogen species can lead to dramatic changes in the oxidative capacity of the overlying atmosphere. At ambient pH and naturally occurring halide concentrations, the dark ozonation of NaBr and NaI solutions was found to proceed more quickly on frozen vs. aqueous substrates, consistent with a freeze-concentration enhancement in halide concentration at the surface. A photochemical mechanism for halogen release from artificial saline snow was evidenced. The presence of ozone and light in the actinic region leads to accelerated production of Br2 and BrCl and the release of Cl2, in a process enhanced by high surface area, acidity and additional gas phase Br2. The results provide strong evidence for snowpack "halogen explosion" chemistry in which gas phase halogens are recycled back into a concentrated brine layer at the snow grain surface.

Although the air-ice interface is atmospherically important, it is difficult to model accurately because exclusion and precipitation of solutes during freezing, deposition of atmospheric species, and heterogeneous/photochemical processes all affect its properties. In this thesis, glancing-angle spectroscopic methods were developed to study ice surfaces. Glancing-angle Raman spectroscopy showed that nitrate is not strongly excluded to the ice surface during freezing, in contradiction with expectations based on equilibrium thermodynamics. Glancing-angle laser-induced fluorescence showed that hydronium ions are not strongly excluded when dilute acidic solutions (HNO3 or HCl) are frozen. These results suggest that solutes are not universally excluded and that care should be taken in modelling surface concentrations on ice. Deposition of HCl(g) was found to result in different pH responses at the "pure" vs. "salty" ice surfaces. Changes at the "salty" ice surface were consistent with the existence of a brine layer at the air-ice interface while changes at the "pure" ice surface were distinctly different, indicating that it may not be appropriate to model it as a cold, liquid layer. Significantly, results also suggest that the sea ice surface is buffered against pH changes, with important implications for interpreting pH-dependent chemistry. The conversion of sea-salt derived halides to reactive halogen species can lead to dramatic changes in the oxidative capacity of the overlying atmosphere. At ambient pH and naturally occurring halide concentrations, the dark ozonation of NaBr and NaI solutions was found to proceed more quickly on frozen vs. aqueous substrates, consistent with a freeze-concentration enhancement in halide concentration at the surface. A photochemical mechanism for halogen release from artificial saline snow was evidenced. The presence of ozone and light in the actinic region leads to accelerated production of Br2 and BrCl and the release of Cl2, in a process enhanced by high surface area, acidity and additional gas phase Br2. The results provide strong evidence for snowpack "halogen explosion" chemistry in which gas phase halogens are recycled back into a concentrated brine layer at the snow grain surface.

Oxidation of aqueous bromide into reactive, gas-phase bromine species has been of interest since the 1980’s, when the presence of bromine in the Arctic boundary layer was linked to ozone depletion events. We have investigated two different mechanisms for Br2 release from sea ice. We have shown that nitrate in sea ice can photolyze to produce OH, which can go on to form gas-phase Br2. This reaction is analogous to a known reaction that occurs in the aqueous phase. We have also investigated Br2 production from a heterogeneous reaction between gas-phase ozone and sea ice/seawater. We have determined ozone’s reactive uptake coefficient, and have shown how it varies with temperature, bromide concentration, ozone concentration and acidity. We have been able to decouple the bulk aqueous chemistry that occurs from the Langmuir-Hinshelwood surface chemistry, and quantify the relative contribution of each.

Oxidation of aqueous bromide into reactive, gas-phase bromine species has been of interest since the 1980’s, when the presence of bromine in the Arctic boundary layer was linked to ozone depletion events. We have investigated two different mechanisms for Br2 release from sea ice. We have shown that nitrate in sea ice can photolyze to produce OH, which can go on to form gas-phase Br2. This reaction is analogous to a known reaction that occurs in the aqueous phase. We have also investigated Br2 production from a heterogeneous reaction between gas-phase ozone and sea ice/seawater. We have determined ozone’s reactive uptake coefficient, and have shown how it varies with temperature, bromide concentration, ozone concentration and acidity. We have been able to decouple the bulk aqueous chemistry that occurs from the Langmuir-Hinshelwood surface chemistry, and quantify the relative contribution of each.

Glancing angle laser induced fluorescence was used to monitor the kinetics of the photodegradation of chlorophyll at the surface of various salt solutions. The loss was measured using varying wavelengths of actinic radiation in the presence and absence of gas phase ozone. The loss rate of illuminated chlorophyll was faster on salt water surfaces than fresh water surfaces, both in the presence and absence of ozone. On salt water surfaces, the dependence of the loss rate on [O3(g)] was different under illuminated conditions than in the dark. This was further investigated by measuring the excitation spectra and the dependence of chlorophyll loss on the concentration of salts at the salt water surface. The possible production of reactive halogen atoms is the likely reason for the observed enhancement. The following results provide evidence of photosensitized oxidation of halogen anions, in the UV-visible range of the spectrum, resulting in halogen atom release.

The work presented in this thesis explores the optical properties of hierarchical structures composed of nanoscale building blocks ranging from metals to semiconductors and composites, organized through bottom-up design methods. 1) By following the dynamic generation of hot-spots in self-assembled chains of gold nanorods (NRs), we have established a direct correlation between ensemble-averaged surface-enhanced Raman scattering (SERS) and extinction properties of these nanoscale chains. Experimental results were supported by comprehensive finite-difference time-domain simulations (FDTD). The relationship established between the structure of nanorod ensembles and their optical properties provides a basis for producing dynamic, solution-based, plasmonic platforms for applications ranging from sensing to nanoelectronics. 2) We report theoretical and experimental analyses of the optical properties of side-by-side assembled gold NRs. Comprehensive FDTD simulations showed a blue shift of the surface plasmon resonance in the side-by-side assembled NR structures and a reduction of electric field intensity as the number of NRs per stack increased. These results were experimentally verified via extinction measurements and ensemble-averaged SERS spectroscopy. The experimental results and electrodynamic simulations were found to be in agreement. 3) The efficacy of hollow core photonic crystal fibers (HCPCF) as a platform for SERS spectroscopy was demonstrated. SERS measurements carried out using this platform showed the capability to monitor minute amounts of ligands on the surface of gold nanoparticles and SERS signals from HCPCF exhibited a 10-fold enhancement. Using the exchange of cetyltrimethylammonium bromide with α-methoxy-ω mercaptopolyethylene glycol on the surface of gold nanorods as an exemplary system, we showed the feasibility of using HCPCF SERS to monitor the change in surface chemistry of NRs. 4) Facile, solution-phase formation of ordered, lamellar quantum dot (QD) arrays exhibiting structural integrity and temporal stability, without the need for chemical crosslinking, was achieved. While micrometers in diameter, they are typically only two to three QD layers thick. These structures are capable of carrying a cargo of water-soluble ions, molecules, metal nanoparticles, or biomolecules. The photoluminescence of the host CdSe QDs were enhanced by the encapsulation of gold nanoparticles within the lamellae, demonstrating the ability to modulate their properties through the cargo they carry. 5) This chapter explores a bottom-up method to produce a metamaterial designed to function as an optical cloak in the visible range. A composite material consisting of an array of silver nanowires (NWs) in a dielectric host has been produced based on the theory of a non-magnetic optical cloak. The required radial array of silver NWs was achieved by electroless deposition of the metal into the channels of a porous alumina structure grown perpendicularly from the curved surface of a micrometer scale aluminum wire. The functionality of the cloak was demonstrated by partial cloaking in the visible range (540 nm).

Collagen is one of the major protein constituents in mammals and is present in all tissues and organs with the exceptions of keratin tissues such as hair and nails. Collagen monomers self-aggregate into a number of structures. In order to understand the physical bases for the structural polymorphism observed in collagen, a good starting point is one of the simplest collagen aggregates, segmental long spacing (SLS) collagen. Although SLS collagen formation induced by the presence of adenosine 5’-triphosphate is widely known, effects of other triphosphates, on the other hand, are much less studied. By varying the pH, it is discovered that all the nucleoside 5’-triphophsates, as well as inorganic triphosphate, are able to induce SLS formation over certain pH ranges. Adenosine 5’-diphosphate and para-nitrophenylphosphate cannot induce SLS formation at any pH. Based on the pH ranges at which SLS collagen can be formed, it is concluded the triphosphate functionality, with one negative charge per phosphate group, is primarily responsible for the formation of SLS collagen. Since inorganic triphosphate is able to induce SLS collagen formation, the presence of the nucleoside is optional for the assembly process; however if present, the assembly process prefers the nucleosides carrying acidic protons. Using electron spectroscopic imaging (ESI) technique, it is found phosphorus, present only in nucleotides but not in polypeptides, is localized in certain regions of SLS collagen, forming a unique banding pattern transverse the long axis of the SLS collagen. Nitrogen mapping indicates the localization of phosphorus is not due to accumulation of materials. The phosphorus banding pattern demonstrates an excellent consistency across SLS collagen assembled from both bovine and recombinant human collagen monomers. Results from molecular simulation are consistent with the experimental results. All threephosphate groups seem to be involved in the assembly process to some degree. In the last chapter of the thesis, a reliable protocol to synthesis native type collagen fibers is introduced.