Development and optimisation of photonic crystal based nanosensors

This thesis involved the development of two Biosensors and their associated assays for the detection of diseases, namely IBR and BVD for veterinary use and C1q protein as a biomarker to pancreatic cancer for medical application, using Surface Plasmon Resonance (SPR) and nanoplasmonics. SPR techniques have been used by a number of groups, both in research [1-3] and commercially [4, 5] , as a diagnostic tool for the detection of various biomolecules, especially antibodies [6-8]. The biosensor market is an ever expanding field, with new technology and new companies rapidly emerging on the market, for both human [8] and veterinary applications [9, 10]. In Chapter 2, we discuss the development of a simultaneous IBR and BVD virus assay for the detection of antibodies in bovine serum on an SPR-2 platform. Pancreatic cancer is the most lethal cancer by organ site, partially due to the lack of a reliable molecular signature for diagnostic testing. C1q protein has been recently proposed as a biomarker within a panel for the detection of pancreatic cancer. The third chapter discusses the fabrication, assays and characterisation of nanoplasmonic arrays. We will talk about developing C1q scFv antibody assays, clone screening of the antibodies and subsequently moving the assays onto the nanoplasmonic array platform for static assays, as well as a custom hybrid benchtop system as a diagnostic method for the detection of pancreatic cancer. Finally, in chapter 4, we move on to Guided Mode Resonance (GMR) sensors, as a low-cost option for potential use in Point-of Care diagnostics. C1q and BVD assays used in the prior formats are transferred to this platform, to ascertain its usability as a cost effective, reliable sensor for diagnostic testing. We discuss the fabrication, characterisation and assay development, as well as their use in the benchtop hybrid system.

Hardware processors for pairing-based cryptography

Bilinear pairings can be used to construct cryptographic systems with very desirable properties. A pairing performs a mapping on members of groups on elliptic and genus 2 hyperelliptic curves to an extension of the finite field on which the curves are defined. The finite fields must, however, be large to ensure adequate security. The complicated group structure of the curves and the expensive field operations result in time consuming computations that are an impediment to the practicality of pairing-based systems. The Tate pairing can be computed efficiently using the ɳT method. Hardware architectures can be used to accelerate the required operations by exploiting the parallelism inherent to the algorithmic and finite field calculations. The Tate pairing can be performed on elliptic curves of characteristic 2 and 3 and on genus 2 hyperelliptic curves of characteristic 2. Curve selection is dependent on several factors including desired computational speed, the area constraints of the target device and the required security level. In this thesis, custom hardware processors for the acceleration of the Tate pairing are presented and implemented on an FPGA. The underlying hardware architectures are designed with care to exploit available parallelism while ensuring resource efficiency. The characteristic 2 elliptic curve processor contains novel units that return a pairing result in a very low number of clock cycles. Despite the more complicated computational algorithm, the speed of the genus 2 processor is comparable. Pairing computation on each of these curves can be appealing in applications with various attributes. A flexible processor that can perform pairing computation on elliptic curves of characteristic 2 and 3 has also been designed. An integrated hardware/software design and verification environment has been developed. This system automates the procedures required for robust processor creation and enables the rapid provision of solutions for a wide range of cryptographic applications.