Surface plasmon resonance (SPR) sensors provide high sensitivity without the use of molecular labels. Most commercial SPR biosensors are based on the simple, robust and highly sensitive traditional prism-coupled configuration. However, they are not amenable to miniaturization and integration. This has led to a growing interest in the development of robust, portable and highly sensitive SPR sensing devices capable of out of laboratory measurements. This thesis covers the modelling of these sensors, using the full vectorial finite element and the eigenmode expansion methods with the aim of optimising the proposed sensors for operation in aqueous environments. The thesis focuses on designs based on photonic crystal fibres and planar waveguides to achieve highly sensitive and compact platforms capable of multi analyte I channel operation. It is no longer feasible to optimise designs by simply fabricating and testing a large set of possible alternatives. This can be time consuming for complex devices such as SPR sensors. This requires computer models which can simulate the behaviour of the different designs in an accurate and speedy manner. This will make it possible to accurately predict device performance characteristics for different material and structural configurations, thereby affording designers the opportunity to experiment with different system configurations for optimal performance. In order to maintain modelling accuracy, all materials are modelled as dispersive and a full-wave analysis is undertaken. to account for the important frequency dependent effects. At every stage in this research, .,care was taken to bench-mark our results against the best available data, whether numerical or analytical whenever available, in order to validate our work. The effects of structural and material parameters on sensor performance metrics such as sensitivity are thoroughly investigated to arrive at optimised designs.

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A broadband terahertz time-domain system (THz-TDS) has been developed in order to analyse several drugs-of-abuse and explosives in the terahertz region of the electromagnetic spectrum. Many of the samples analysed, showed numerous spectral features in the terahertz region, which could be used to conclusively identify them; using terahertz spectroscopy. Terahertz spectra are also compared to Raman spectra in the same frequency region. Comparison of these spectra shows that there are often significant spectral differences, . which provides information about the relative activity of the THz and Raman active modes, which in tum can be useful in the identification of the origin of the normal modes. The normal modes of many of the molecules analysed have also been calculated using . both molecular mechanics (MM) and quantum mechanical (QM) codes, in on;ler to predict the terahertz spectra of the compounds, and to gain a fundamental understanding of the origin of the normal modes. Drugs-of-abuse and explosives found in the real world are often impure or diluted, so . real world 'street samples' and plastics explosives have also been analysed to determine the effect of a mixture of adulterants, on the terahertz spectra of a compound and whether· this will prohibit the identification. This data has also been combined with chemometric based techniques such as principal component analysis (PCA) in order to start moving towards a system for the automatic identification of a compound using terahertz spectroscopy. Finally, an analysis of a drug sample through a range of common packaging materials, using THz-TDS, has also been performed in order to determine if drugs-of-abuse can be detected through packaging.

Copper-containing nitrite reductases (NiRs) are enzymes that efficiently reduce nitrite to nitric oxide in potent denitrifying bacteria. There has been an interest in their application in amperometric biosensors for monitoring nitrite levels in natural and waste waters. NiRs have a complex enzyme mechanism and depend on nitrite concentration and pH. Although the mechanism has been intensively studied, it is still controversial. In this thesis, a combined fluorescence and electrochemical method is used to simultaneously monitor the nitrite turn-over rate of a NiR from Alcaligenes faecalis S-6 and the oxidation state of the type-1 copper electron transfer site inside the enzyme. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labelled enzyme molecules immobilised on modified gold, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by F6rster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. Here, a determining role of internal electron transfer is found in NiR's mechanism. Moreover, the heterogeneous interfacial electron transfer to adsorbed NiRs is observed. The electro- activity and binding of labelled and unlabelled NiRs on gold modified with different self-assembled monolayers (SAMs) are studied to understand the effect of NiR labelling on the protein-electrode interactions. Here, electro-active and well-ordered biofilms of NiRs are found on electrodes with SAMs carrying the positive charge (negative NiRs) or when NiRs are modified with fluorophores that help orienting them on SAM-modified gold. Attempts have also been made to implement fluorescently labelled NiRs into the biosensor-like device with a fluorescence output using gold electrodes modified with tethered lipid bilayers (tBLMs) or conducting polymers (CPs). In spite of being unsuccessful, these studies give a better understanding of potential-dependent polymer dynamics and a control over protein immobilisation on functionalised lipid bilayer platforms.

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