Theses
This collection is licenced under a Creative Commons licence. The collection may be reproduced for noncommerical use and without modification, providing that copyright is acknowledged.
Recent Submissions

A Framework for WebBased Immersive AnalyticsThe emergence of affordable Virtual Reality (VR) interfaces has reignited the interest of researchers and developers in exploring new, immersive ways to visualise data. In particular, the use of openstandards Webbased technologies for implementing VR experiences in a browser aims to enable their ubiquitous and platformindependent adoption. In addition, such technologies work in synergy with established visualization libraries, through the HTML Document Object Model (DOM). However, creating Immersive Analytics (IA) experiences remains a challenging process, as the systems that are currently available require knowledge of game engines, such as Unity, and are often intrinsically restricted by their development ecosystem. This thesis presents a novel approach to the design, creation and deployment of Immersive Analytics experiences through the use of openstandards Web technologies. It presents <VRIA>, a Webbased framework for creating Immersive Analytics experiences in VR that was developed during this PhD project. <VRIA> is built upon WebXR, AFrame, React and D3.js, and offers a visualization creation workflow which enables users of different levels of expertise to rapidly develop Immersive Analytics experiences for the Web. The aforementioned reliance on open standards and the synergies with popular visualization libraries make <VRIA> ubiquitous and platformindependent in nature. Moreover, by using WebXR’s progressive enhancement, the experiences <VRIA> is able to create are accessible on a plethora of devices. This thesis presents an elaboration on the motivation for focusing on openstandards Web technologies, presents the <VRIA> visualization creation workflow and details the underlying mechanics of our framework. It reports on optimisation techniques, integrated into <VRIA>, that are necessary for implementing Immersive Analytics experiences with the necessary performance profile on the Web. It discusses scalability implications of the framework and presents a series of use case applications that demonstrate the various features of <VRIA>. Finally, it describes the lessons learned from the development of the framework, discusses current limitations, and outlines further extensions.

Efficient Surrogate ModelAssisted Evolutionary Algorithm for Electromagnetic Design Automation with ApplicationsIn this thesis, the surrogate modelaware evolutionary search (SMAS) framework is extended for efficient interactive optimisation of multiple criteria electromagnetic (EM) designs and/or devices through a novel method called twostage interactive efficient EM microactuator design optimisation (TIEMO). The first robust analytical and behavioural study of the SMAS framework is also carried out in this thesis to serve as a guide for the meticulous selection of multiple differential evolution (DE) mutation strategies to make SMAS fit for use in parallel computing environments. Based on the study of SMAS and the selfadaptive use of the selected multiple DE mutation strategies and reinforcement learning techniques, a novel method, parallel surrogate modelassisted evolutionary algorithm for EM design (PSAED) is proposed. PSAED is tested extensively using mathematical benchmark problems and numerical EM design problems. For all cases, the efficiency improvement of PSAED compared to stateoftheart evolutionary algorithms (EAs) is demonstrated by the several times up to about 20 times speed improvement observed and the high quality of design solutions. PSAED is then applied to realworld EM design problems as two purposebuilt methods for antenna design and optimisation and highperformance microelectromechanical systems (MEMS) design and optimisation in parallel computing environments, parallel surrogate modelassisted hybrid DE for antenna optimisation (PSADEA) and adaptive surrogate modelassisted differential evolution for MEMS optimisation (ASDEMO), respectively. For all the realworld antenna and MEMS design cases, PSAED methods obtain very satisfactory design solutions using an affordable optimisation time and comparisons are made with available alternative methods. Results from the comparisons show that PSAED methods obtain very satisfactory design solutions in all runs using an affordable optimisation time in each, whereas the alternative methods fail and/or seldom succeed to obtain feasible or satisfactory design solutions. PSAED methods also show better robustness and stability. In the future, PSAED methods will be embedded into commercial CAD/CEM tools and will be further extended for use in higherorder parallel clusters.

Mathematical Modelling of DNA MethylationDNA methylation is a key epigenetic process which has been intimately associated with gene regulation. In recent years growing evidence has associated DNA methylation status with a variety of diseases including cancer, Alzheimer’s disease and cardiovascular disease. Moreover, changes to DNA methylation have also recently been implicated in the ageing process. The factors which underpin DNA methylation are complex, and remain to be fully elucidated. Over the years mathematical modelling has helped to shed light on the dynamics of this important molecular system. Although the existing models have contributed significantly to our overall understanding of DNA methylation, they fall short of fully capturing the dynamics of this process. In this work DNA methylation models are developed and improved and their suitability is demonstrated through mathematical analysis and computational simulation. In particular, a linear and nonlinear deterministic model are developed which capture more fully the dynamics of the key intracellular events which characterise DNA methylation. Furthermore, uncertainty is introduced into the model to describe the presence of intrinsic and extrinsic cell noise. This way a stochastic model is constructed and presented which accounts for the stochastic nature in cell dynamics. One of the key predictions of the model is that DNA methylation dynamics do not alter when the quantity of DNA methylation enzymes change. In addition, the nonlinear model predicts DNA methylation promoter bistability, which is commonly observed experimentally. Moreover, a new way of modelling DNA methylation uncertainty is introduced.

Motion of a space tether system in the atmosphereThe space tether system under consideration consists of two rigid bodies with significantly different ballistic coefficients. Because of this difference one of the bodies acts as a stabilizer for the main body – a spacecraft – during the motion of the tether system in the atmosphere. The investigations are focused on the stability of motion of the tether system in the atmosphere. During its motion in the atmosphere the tether system makes use of torques from aerodynamic forces to maintain a desired orientation. This aerodynamic method of stabilization is passive and does not require energy expenses. Such a tether system can be used to stabilize the motion before landing onto the surface of Earth or other planets with atmospheres. The aerodynamic tether system is helpful for returning payloads from outer space, especially using small landing modules. It is also possible to utilize in the removal of space debris by reducing the altitude of their orbits. By achieving the spacecraft motion stability during descent the tether system enables a reduction in the target landing area at the final stage of the descent. The modelling of motion of the tether system includes two parts – (i) the deployment of the tether system, and (ii) the descent of deployed tether system through the dense layers of the atmosphere. The motion of the deployed tether system is investigated with regard to the terms of its stability. The tether system can be in stable motion even if either or both bodies are statically unstable. The stability of the system is assessed relative to the parameters – the mass, the geometrical dimensions of the bodies and the length of the tether. It is found that increasing the length of the tether, as a controlled part of the deployment process during descent, can provide an additional stabilizing factor for the tether system. The model of the deployment process, based on the model of an elastic tether, represents the tether as a set of nodes with mass and with elastic connections. The control of the deployment is based on the length and the rate of change of the length of the tether. The aerodynamic resistance of the tether and its mass characteristics are both taken into consideration during modelling of the deployment. The described and numerically realized mathematical models allows the parameters for the space tether system motion in the atmosphere to be determined.

Investigation of size, concentration and particle shapes in hydraulic systems using an inline CMOS image matrix sensorThe theoretical and experimental investigation of the novel inline CMOS image sensor was performed. This sensor is aimed to investigate particle size distribution, particle concentration and shape in hydraulic liquid in order to implement the proactive maintenance of hydraulic equipment. The existing instruments such as automatic particle counters and techniques are not sufficiently enough to address this task because of their restricted sensitivity, limit of concentration to be measured and they cannot determine particle shape. Other instruments cannot be used as inline sensors because they are not resistant to the arduous conditions such as high pressure and vibration. The novel mathematical model was proposed as it is not possible to use previously developed techniques based on using optical system and complicated algorithms. This model gives the output signal of the image sensor depending on the particle size, its distance from the light source (LED) and image sensor. Additionally, the model takes into account the limited exposure time and particle track simulation. The results of simulation based on the model are also performed in thesis. On the basis of the mathematical model the image processing algorithms were suggested in order to determine particle size even when this size is lower than pixel size. There are different approaches depending on the relation between the size of the particle and the pixel size. The approach to the volume of liquid sample estimation was suggested in order to address the problem of low accuracy of concentration measurement by the conventional automatic particle counters based on the single photodiode. Proposed technique makes corrections on the basis of particle velocity estimation. Approach to the accuracy estimation of the sensor was proposed and simulation results are shown. Generally, the accuracy of particle size and concentration measurement was considered. Ultimately, the experimental setup was used in order to test suggested techniques. The mathematical model was tested and the results showed sufficient correlation with the experiment. The zinc dust was used as a reference object as there are the particles within the range from 1 to 25 microns which is appropriate to check the sensitivity. The results of experiments using reference instrument showed the improved sensitivity and accuracy of volume measured compared to the reference one.

Numerical Solution of Fractional Differential Equations and their Application to Physics and EngineeringThis dissertation presents new numerical methods for the solution of fractional differential equations of single and distributed order that find application in the different fields of physics and engineering. We start by presenting the relationship between fractional derivatives and processes like anomalous diffusion, and, we then develop new numerical methods for the solution of the timefractional diffusion equations. The first numerical method is developed for the solution of the fractional diffusion equations with Neumann boundary conditions and the diffusivity parameter depending on the space variable. The method is based on finite differences, and, we prove its convergence (convergence order of O(Δx² + Δt²<sup>α</sup>), 0 < α < 1) and stability. We also present a brief description of the application of such boundary conditions and fractional model to real world problems (heat flux in human skin). A discussion on the common substitution of the classical derivative by a fractional derivative is also performed, using as an example the temperature equation. Numerical methods for the solution of fractional differential equations are more difficult to develop when compared to the classical integerorder case, and, this is due to potential singularities of the solution and to the nonlocal properties of the fractional differential operators that lead to numerical methods that are computationally demanding. We then study a more complex type of equations: distributed order fractional differential equations where we intend to overcome the second problem on the numerical approximation of fractional differential equations mentioned above. These equations allow the modelling of more complex anomalous diffusion processes, and can be viewed as a continuous sum of weighted fractional derivatives. Since the numerical solution of distributed order fractional differential equations based on finite differences is very time consuming, we develop a new numerical method for the solution of the distributed order fractional differential equations based on Chebyshev polynomials and present for the first time a detailed study on the convergence of the method. The third numerical method proposed in this thesis aims to overcome both problems on the numerical approximation of fractional differential equations. We start by solving the problem of potential singularities in the solution by presenting a method based on a nonpolynomial approximation of the solution. We use the method of lines for the numerical approximation of the fractional diffusion equation, by proceeding in two separate steps: first, spatial derivatives are approximated using finite differences; second, the resulting system of semidiscrete ordinary differential equations in the initial value variable is integrated in time with a nonpolynomial collocation method. This numerical method is further improved by considering graded meshes and an hybrid approximation of the solution by considering a nonpolynomial approximation in the first subinterval which contains the origin in time (the point where the solution may be singular) and a polynomial approximation in the remaining intervals. This way we obtain a method that allows a faster numerical solution of fractional differential equations (than the method obtained with nonpolynomial approximation) and also takes into account the potential singularity of the solution. The thesis ends with the main conclusions and a discussion on the main topics presented along the text, together with a proposal of future work.