This thesis examines the synthesis of conformationally constrained β-amino acids and β- peptides, and the electron transfer properties of the latter when immobilised on gold. Additionally, cross metathesis on gold was investigated as a method for surface functionalisation. Chapter One introduces the concepts of electron transfer in nature, how it is facilitated by the secondary structure in α-peptides, and why β-peptides might be useful for studying electron transfer. This is followed by a discussion of the properties of β-peptides, including the enhanced stability and variety of helical secondary structures and the greater potential for functionalisation of the peptide backbone when compared to α-peptides. Finally, the conformational constraints of ring-systems on cyclic amino acids is discussed, with reference to the stabilising effect of these compounds on peptide secondary structures. Chapter Two describes the electrochemical analysis of β-hexapeptides immobilised on gold. The chapter is prefaced by a discussion of the important electron transfer mechanisms for peptides, the fabrication of peptide-gold self-assembled monolayer (SAM) interfaces, and the electron transfer in helical α-peptides. β-Peptides containing an electroactive ferrocene moeity were immobilised on gold and studied using cyclic voltammetry and chronoamperometry. The latter method was used to examine the dependence of the electron transfer rate on overpotential, thereby determining the likely mode of electron transfer through the β-peptides SSβ₆Fc, Fcβ₆SS and SC₁₅β₆Fc. These peptides exhibited very weak dependence on overpotential, characteristic of electron transfer behaviour of an electron hopping mechanism (which is also thought to occur in helical α-peptides). Both the dipole moment of the peptides and the structure of the sulfurlinker group were found to be important in determining the rate of electron transfer. Conversely, the equivalent α-peptide SSα₆Fc exhibited electron transfer behaviour characteristic of the less efficient tunnelling mechanism, which is thought to operate in strand-like peptides. Chapter Three examines the application of cross metathesis, using a Grubbs' second generation catalyst, as a means to functionalise olefin-terminated self-assembled monolayers on gold. Abstract iv Firstly, an introduction into the limited published research on cross metathesis on both planar surfaces and nanoparticles is given. Olefin-terminated thiol 3.18, suitable for immobilisation on gold, and solution phase olefin-terminated ferrocene 3.10 were synthesised as reactants for cross metathesis studies. An analytical methodology was developed involving the cross metathesis of surface-immobilised 3.18 with ferrocene 3.10 in dichloromethane, whereby the concentration of electroactive cross metathesis product 3.22 was monitored electrochemically as a function of time. The concentration of surface-immobilised product 3.22 was determined by integration of the oxidation peak area and found to be highly dependent on both the concentration of immobilised olefin reactant 3.18 and reaction time. Furthermore, the surface concentration of ferrocenyl model disulfide 3.21 and thiol 2.18 decayed markedly upon addition of Grubb's catalyst, as revealed by the decrease in the oxidation peak area, which suggested that catalystmediated desorption was occurring. Chapter Four details the solution-phase synthesis of ferrocene- and thiol-functionalised β- hexapeptides used in both the electron transfer studies described in chapter two, and in the determination of secondary structure using circular dichroism and NMR techniques. The synthesis of simple model compounds 4.14, 4.16 and 4.18 established the incompatibility of the deprotection of methyl and benzyl ester protecting groups with protected-thiol and disulfide linkers, leading to the use of N-hydroxysuccinmide-activated sulfur-linkers 4.20 and 4.22 in further synthesis. A number of β-hexapeptides were synthesised by amide coupling of β- tripeptides functionalised at the N- and C-termini. Structural studies of the methanol soluble β- hexapeptide 4.60 suggested that the covalent attachment of ferrocene moeity to the C-terminus of a β-peptide did not disrupt the formation of a 14-helix in solution. β-peptides containing functionality at both the C- and N-termini (such as SSβ₆Fc, SSβ₆Et and acetyl-protected SC₁₅β₆Fc) were not suitable for solution phase structural studies; however, molecular modelling suggested that helical conformations are the most stable these β-peptides in solution phase. Chapter Five outlines the synthesis of novel cyclic β-amino acids by two different general synthetic routes. The first uses an efficient conjugate addition/fluorination reaction of α,β- unsaturated esters with lithiated chiral secondary amines to prepare the novel cyclopentyl- and cyclohexyl-based fluorinated β-amino acids 2.43a and 2.43b. The high diastereoselectivity of this reaction, which introduces two stereocentres into the achiral unsaturated esters, is directed by the configuration of the attacking amine. The second methodology utilizes the versatile ringclosing metathesis reaction in the synthesis of novel cyclic β-amino acids. A stereoselective Abstract v trans-alkylation of olefinic β-amino acids gave the required β-dienes 5.62 and 5.77. Optimised cyclisation yields were achieved with a Grubb's 2nd generation catalyst for diene 5.62 and Grubb's 1st generation catalyst for diene 5.77, to give the trans-cycloheptyl- and cyclooctylbased β-amino acids 5.63 and 5.78, respectively. The attempted synthesis of cyclononyl-based β-amino acid 5.87 using both catalysts yielded only cyclic dimer products 5.88 and 5.89. The trans configuration of the 5.62 diene was confirmed by x-ray crystallography. Chapter Six is an experimental chapter and outlines the electrochemical setup and analysis, and the synthesis, purification and characterisation of compounds described in this thesis.

This thesis examines the synthesis of conformationally constrained β-amino acids and β- peptides, and the electron transfer properties of the latter when immobilised on gold. Additionally, cross metathesis on gold was investigated as a method for surface functionalisation. Chapter One introduces the concepts of electron transfer in nature, how it is facilitated by the secondary structure in α-peptides, and why β-peptides might be useful for studying electron transfer. This is followed by a discussion of the properties of β-peptides, including the enhanced stability and variety of helical secondary structures and the greater potential for functionalisation of the peptide backbone when compared to α-peptides. Finally, the conformational constraints of ring-systems on cyclic amino acids is discussed, with reference to the stabilising effect of these compounds on peptide secondary structures. Chapter Two describes the electrochemical analysis of β-hexapeptides immobilised on gold. The chapter is prefaced by a discussion of the important electron transfer mechanisms for peptides, the fabrication of peptide-gold self-assembled monolayer (SAM) interfaces, and the electron transfer in helical α-peptides. β-Peptides containing an electroactive ferrocene moeity were immobilised on gold and studied using cyclic voltammetry and chronoamperometry. The latter method was used to examine the dependence of the electron transfer rate on overpotential, thereby determining the likely mode of electron transfer through the β-peptides SSβ₆Fc, Fcβ₆SS and SC₁₅β₆Fc. These peptides exhibited very weak dependence on overpotential, characteristic of electron transfer behaviour of an electron hopping mechanism (which is also thought to occur in helical α-peptides). Both the dipole moment of the peptides and the structure of the sulfurlinker group were found to be important in determining the rate of electron transfer. Conversely, the equivalent α-peptide SSα₆Fc exhibited electron transfer behaviour characteristic of the less efficient tunnelling mechanism, which is thought to operate in strand-like peptides. Chapter Three examines the application of cross metathesis, using a Grubbs' second generation catalyst, as a means to functionalise olefin-terminated self-assembled monolayers on gold. Abstract iv Firstly, an introduction into the limited published research on cross metathesis on both planar surfaces and nanoparticles is given. Olefin-terminated thiol 3.18, suitable for immobilisation on gold, and solution phase olefin-terminated ferrocene 3.10 were synthesised as reactants for cross metathesis studies. An analytical methodology was developed involving the cross metathesis of surface-immobilised 3.18 with ferrocene 3.10 in dichloromethane, whereby the concentration of electroactive cross metathesis product 3.22 was monitored electrochemically as a function of time. The concentration of surface-immobilised product 3.22 was determined by integration of the oxidation peak area and found to be highly dependent on both the concentration of immobilised olefin reactant 3.18 and reaction time. Furthermore, the surface concentration of ferrocenyl model disulfide 3.21 and thiol 2.18 decayed markedly upon addition of Grubb's catalyst, as revealed by the decrease in the oxidation peak area, which suggested that catalystmediated desorption was occurring. Chapter Four details the solution-phase synthesis of ferrocene- and thiol-functionalised β- hexapeptides used in both the electron transfer studies described in chapter two, and in the determination of secondary structure using circular dichroism and NMR techniques. The synthesis of simple model compounds 4.14, 4.16 and 4.18 established the incompatibility of the deprotection of methyl and benzyl ester protecting groups with protected-thiol and disulfide linkers, leading to the use of N-hydroxysuccinmide-activated sulfur-linkers 4.20 and 4.22 in further synthesis. A number of β-hexapeptides were synthesised by amide coupling of β- tripeptides functionalised at the N- and C-termini. Structural studies of the methanol soluble β- hexapeptide 4.60 suggested that the covalent attachment of ferrocene moeity to the C-terminus of a β-peptide did not disrupt the formation of a 14-helix in solution. β-peptides containing functionality at both the C- and N-termini (such as SSβ₆Fc, SSβ₆Et and acetyl-protected SC₁₅β₆Fc) were not suitable for solution phase structural studies; however, molecular modelling suggested that helical conformations are the most stable these β-peptides in solution phase. Chapter Five outlines the synthesis of novel cyclic β-amino acids by two different general synthetic routes. The first uses an efficient conjugate addition/fluorination reaction of α,β- unsaturated esters with lithiated chiral secondary amines to prepare the novel cyclopentyl- and cyclohexyl-based fluorinated β-amino acids 2.43a and 2.43b. The high diastereoselectivity of this reaction, which introduces two stereocentres into the achiral unsaturated esters, is directed by the configuration of the attacking amine. The second methodology utilizes the versatile ringclosing metathesis reaction in the synthesis of novel cyclic β-amino acids. A stereoselective Abstract v trans-alkylation of olefinic β-amino acids gave the required β-dienes 5.62 and 5.77. Optimised cyclisation yields were achieved with a Grubb's 2nd generation catalyst for diene 5.62 and Grubb's 1st generation catalyst for diene 5.77, to give the trans-cycloheptyl- and cyclooctylbased β-amino acids 5.63 and 5.78, respectively. The attempted synthesis of cyclononyl-based β-amino acid 5.87 using both catalysts yielded only cyclic dimer products 5.88 and 5.89. The trans configuration of the 5.62 diene was confirmed by x-ray crystallography. Chapter Six is an experimental chapter and outlines the electrochemical setup and analysis, and the synthesis, purification and characterisation of compounds described in this thesis.

No description available.

Black hole-neutron star (BH-NS) mergers are promising candidates for the progenitors of short-duration gamma-ray bursts (GRBs). With the right initial conditions, the neutron star becomes tidally disrupted, eventually forming a dense, accreting disk around the black hole. The thermal energy of this black hole-disk system can be extracted via neutrino processes, while the spin energy of the black hole can be extracted via magnetic processes. Either (or even a combination of these) processes could feasibly power a relativistic jet with energy ≥~ 10 49 erg and duration ≤~ 2 s, hence producing a short-duration GRB. In this thesis, we investigate BH-NS mergers with three-dimensional, pseudo-Newtonian simulations. We use the simulation code Charybdis, which uses a dimensionally-split, reconstruct-solve-average scheme (i.e. using Riemann solvers) to solve the Euler equations of hydrodynamics. Although the code is based on a Newtonian framework, it includes pseudo- Newtonian approximations of local gravitational wave effects and the innermost stable circular orbit of the BH, which are both general relativistic phenomena. The code also includes the effects of global neutrino emission, shear viscosity and self-gravity. This thesis comprises two main projects. The first project is a parameter study of the equation of state, which encapsulates the relationship between the pressure of a fluid and its other thermodynamic properties. Although the EOS is well understood at low densities, it is yet to be constrained at supranuclear densities, and so must be treated as a parameter in numerical studies of BH-NS mergers. We present simulations using three existing EOSs, in order to investigate their effect on the merger dynamics. We find that the EOS strongly influences the fate of the NS, the properties of the accretion disk, and the neutrino emission. In the second project, we begin upgrading Charybdis to include magnetic field effects, in order to investigate the magnetic processes described above. We implement existing reconstruction and Riemann solver algorithms for the equations of magnetohydrodynamics, and present 1D tests to compare them. When modelling magnetic fields in more than one dimension, we must also deal with the divergence-free condition, ∇. B = 0. We develop a new constrained transport algorithm to ensure our code maintains this condition, and present 2D tests to confirm its accuracy. This algorithm has many advantages over existing ones, including easier implementation, greater computational efficiency and better parallelisation. Finally, we present preliminary tests that use these algorithms in simulations of BH-NS mergers.

Modern cryptography responds to the need for security that has arisen with the emergence of communication appliances. However, its adapted integration in the wide variety of existing communication systems has opened new design challenges. Amongst them, this thesis addresses two in particular, related to hardware integration of cryptographic algorithms: constrained environments and side-channel security. In the context of constrained environments, we propose to study the interest of the Scalable Encryption Algorithm SEA for constrained hardware applications. We investigate both the FPGA and ASIC contexts and illustrate, using practical implementation results, the interest of this algorithm. Indeed, we demonstrate how hardware implementations can keep its high scalability properties while achieving interesting implementation figures in comparison to conventional algorithms such as the AES. Next, we deal with three complementary aspects related to side-channel resistance. We first propose a new class of dynamic and differential logic families achieving low-power performance with matched leakage of information to state of-the-art countermeasures. We then discuss a power consumption model for these logic styles and apply it to DyCML implementations. It is based on the use of the isomorphism existing between the gate structures of the implemented functions and the binary decision diagrams describing them. Using this model, we are not only able to predict the power consumption, and therefore attack such implementations, but also to efficiently choose the gate structures achieving the best resistance against this model. We finally study a methodology for the security evaluation of cryptographic applications all along their design and test phases. We illustrate the interest of such a methodology at different design steps and with different circuit complexity, using either simulations or power consumption measurements.

In this thesis we consider solution approaches for the index tacking problem, in which we aim to reproduces the performance of a market index without purchasing all of the stocks that constitute the index. We solve the problem using three different solution approaches: Mixed Integer Programming (MIP), Genetic Algorithms (GAs), and Ant-colony Optimization (ACO) Algorithm by limiting the number of stocks that can be held. Each index is also assigned with different cardinalities to examine the change to the solution values. All of the solution approaches are tested by considering eight market indices. The smallest data set only consists of 31 stocks whereas the largest data set includes over 2000 stocks. The computational results from the MIP are used as the benchmark to measure the performance of the other solution approaches. The Computational results are presented for different solution approaches and conclusions are given. Finally, we implement post analysis and investigate the best tracking portfolios achieved from the three solution approaches. We summarise the findings of the investigation, and in turn, we further improve some of the algorithms. As the formulations of these problems are mixed-integer linear programs, we use the solver ‘Cplex’ to solve the problems. All of the programming is coded in AMPL.

This thesis focuses on securing data exchanged between highly constrained IoT devices and the internet. This thesis builds on existing research by combining elements of different research solutions to create a more secure solution. This solution helps to solve gaps in security left behind by existing solutions through the use of symmetric cryptography in data objects and IoT security gateways which act as intermediaries between devices and the internet. The goal of this research is to provide a security solution for devices which do not have the resources necessary to effectively implement the recommended TLS based protocols for secure communication over the internet. The solution provides confidentiality to data traveling between device and gateway while also providing confidentiality, integrity and authenticity to data traveling across the internet. The solution works by delegating demanding security processes to an IoT security gateway which securely processes communications to and from the internet using HTTPS (SSL/TLS). Security of data being passed between device and gateway is provided with AES symmetric encryption at the Data Link and Data Object layers. The performance of the solution is measured by timing the security process of the IoT device while also measuring the resource requirements of applying the solution to the device. / <p>Validerat; 20150622 (global_studentproject_submitter)</p>

Reaching is a fundamental movement and has been studied widely in the motor control area. To my knowledge no one has directly compared the planning and kinematic characteristics of these two movements. These different definitions of reaching movements may also explain why researchers have reported different results when examining reaching movements of individuals with Autism Spectrum Disorder (ASD). The present study designed three movement types to examine how people with and without ASD plan and execute three different types of reaching movements. The results revealed that typically developing (TD) participants moved faster compared to ASD participants in three dimensional movements, but not in one dimensional and two dimensional movements. Based on the above results it is proposed that the observed difference in movement control resulted from a preference for different sensory feedback for on-line control of limb movements. / October 2015

Given an undirected edge-weighted graph G and a positive integer m, the Constrained Forest Problem (CFP) seeks a lowest-cost (or minimum-weight) forest F which spans G while satisfying the requirement that each tree in F contain at least m vertices. This problem has been shown to be NP-hard for values of m greater than three, giving rise to a number of approximation strategies for finding reasonable m-forest solutions. This research presents a new genetic algorithm (GA) which can consistently find equal-or-better solutions to the problem when compared to non-genetic alternatives. This GA is unique in that it uses chromosomes which are actual candidate solutions (m-forests) and performs genetic operations (random creation, selection, recombination, and mutation) on these candidate solutions. Experiments were run using 180 different GA configurations on 50 benchmark graphs to determine which operators and techniques would be most successful in solving the m-forest problem. The "heaviest edge first" or HEF algorithm run against the minimum spanning tree (MST) of a graph was used as a performance metric. Previously, the HEF(MST) algorithm had been shown to produce the best results on m-forest problems. When the GA was able to find better results than HEF(MST) on the same problem instance, this was considered a GA success. Since the GA's initial population included heuristic candidate solutions such as HEF(MST), the GA never did worse than the best of these. GA solution quality did vary, however, often finding several different better-than-HEF(MST) solutions, illustrating the stochastic nature of the process. Based on data collected from the 9000 initial problem instances, several factors were shown to significantly improve the quality of the GA solution. Problem instances which did not include mutation had a much lower success rate than those which did. Adding calculated heuristic solutions such as HEF(MST) to the initial population allowed the GA to converge more quickly and improved its likelihood of finding better-than-HEF(MST) solutions. Building an initial population using randomly-generated candidate solutions whose edges were restricted to the problem graph's MST proved equally successful. GA configuration options were analyzed using all 9000 test cases and again using only those 403 cases in which the GA was able to find the very best solution for each graph. These analyses were consistent, and resulted in the identification of a single "best" GA configuration which combined the best overall initial population strategy, random seeding algorithms, mutation and crossover strategy. The selected configuration was then further tested using various values of m to ensure that the resulting GA could in fact find better-than-HEF(MST) solutions for the majority of problem instances.

The notion that a universally effective problem solver may still exist, and is simply waiting to be found, is slowly being abandoned in the light of a growing body of work reporting on the narrow applicability of individual heuristics. As the formalism of the constraint satisfaction problem remains a popular choice for the representation of problems to be solved algorithmically, there exists an ongoing need for new algorithms to effciently handle the disparate range of problems that have been posed in this representation. Given the costs associated with manually applying human algorithm development and problem solving expertise, methods that can automatically adapt to the particular features of a specific class of problem have begun to attract more attention. Whilst a number of authors have developed adaptive systems, the field, and particularly with respect to their application to constraint satisfaction problems, has seen only limited discussion as to what features are desirable for an adaptive constraint system. This may well have been a limiting factor with previous implementations, which have exhibited only subsets of the five features identified in this work as important to the utility of an adaptive constraint satisfaction system. Whether an adaptive system exhibits these features depends on both the chosen represen-tation and the method of adaptation. In this thesis, a three-part representation for constraint algorithms is introduced, which defines an algorithm in terms of contention, preference and selection functions. An adaptive system based on genetic programming is presented that adapts constraint algorithms described using the mentioned three-part representation. This is believed to be the first use of standard genetic programming for learning constraint algo-rithms. Finally, to further demonstrate the efficacy of this adaptive system, its performance in learning specialised algorithms for hard, real-world problem instances is thoroughly evaluated. These instances include random as well as structured instances from known-hard benchmark distributions, industrial problems (specifically, SAT-translated planning and cryptographic problems) as well as over-constrained problem instances. The outcome of this evaluation is a set of new algorithms - valuable in their own right - specifically tailored to these problem classes. Partial results of this work have appeared in the following publications: [1] Stuart Bain, John Thornton, and Abdul Sattar (2004) Evolving algorithms for constraint satisfaction. In Proc. of the 2004 Congress on Evolutionary Computation, pages 265-272. [2] Stuart Bain, John Thornton, and Abdul Sattar (2004) Methods of automatic algorithm generation. In Proc. of the 9th Pacific Rim Conference on AI, pages 144-153. [3] Stuart Bain, John Thornton, and Abdul Sattar. (2005) A comparison of evolutionary methods for the discovery of local search heuristics. In Australian Conference on Artificial Intelligence: AI'05, pages 1068-1074. [4] Stuart Bain, John Thornton, and Abdul Sattar (2005) Evolving variable-ordering heuristics for constrained optimisation. In Principles and Practice of Constraint Programming: CP'05, pages 732-736.