http://bura.brunel.ac.uk/handle/2438/149 2013-05-23T14:40:35Z 2013-05-23T14:40:35Z Wu, Zujian http://bura.brunel.ac.uk/handle/2438/7413 2013-05-03T09:26:03Z 2012-01-01T00:00:00Z

Title: A generic approach to behaviour-driven biochemical model construction Authors: Wu, Zujian Abstract: Modelling of biochemical systems has received considerable attention over the last decade from bioengineering, biochemistry, computer science, and mathematics. This thesis investigates the applications of computational techniques to computational systems biology, for the construction of biochemical models in terms of topology and kinetic rates. Due to the complexity of biochemical systems, it is natural to construct models representing the biochemical systems incrementally in a piecewise manner. Syntax and semantics of two patterns are defined for the instantiation of components which are extendable, reusable and fundamental building blocks for models composition. We propose and implement a set of genetic operators and composition rules to tackle issues of piecewise composing models from scratch. Quantitative Petri nets are evolved by the genetic operators, and evolutionary process of modelling are guided by the composition rules. Metaheuristic algorithms are widely applied in BioModel Engineering to support intelligent and heuristic analysis of biochemical systems in terms of structure and kinetic rates. We illustrate parameters of biochemical models based on Biochemical Systems Theory, and then the topology and kinetic rates of the models are manipulated by employing evolution strategy and simulated annealing respectively. A new hybrid modelling framework is proposed and implemented for the models construction. Two heuristic algorithms are performed on two embedded layers in the hybrid framework: an outer layer for topology mutation and an inner layer for rates optimization. Moreover, variants of the hybrid piecewise modelling framework are investigated. Regarding flexibility of these variants, various combinations of evolutionary operators, evaluation criteria and design principles can be taken into account. We examine performance of five sets of the variants on specific aspects of modelling. The comparison of variants is not to explicitly show that one variant clearly outperforms the others, but it provides an indication of considering important features for various aspects of the modelling. Because of the very heavy computational demands, the process of modelling is paralleled by employing a grid environment, GridGain. Application of the GridGain and heuristic algorithms to analyze biological processes can support modelling of biochemical systems in a computational manner, which can also benefit mathematical modelling in computer science and bioengineering. We apply our proposed modelling framework to model biochemical systems in a hybrid piecewise manner. Modelling variants of the framework are comparatively studied on specific aims of modelling. Simulation results show that our modelling framework can compose synthetic models exhibiting similar species behaviour, generate models with alternative topologies and obtain general knowledge about key modelling features. Description: This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.

2012-01-01T00:00:00Z Hussain, Fiaz http://bura.brunel.ac.uk/handle/2438/7397 2013-04-29T09:37:06Z 1991-01-01T00:00:00Z

Title: On the capture and representation of fonts Authors: Hussain, Fiaz Abstract: The commercial need to capture, process and represent the shape and form of an outline has lead to the development of a number of spline routines. These use a mathematical curve format that approximates the contours of a given shape. The modelled outline lends itself to be used on, and for, a variety of purposes. These include graphic screens, laser printers and numerically controlled machines. The latter can be employed for cutting foil, metal. plastic and stone. One of the most widely used software design packages has been the lKARUS system. This, developed by URW of Hamburg (Gennany), employs a number of mathematical descriptions that facilitate the process of both modelling and representation of font characters. It uses a variety of curve formats, including Bezier cubics, general conics and parabolics. The work reported in this dissertation focuses on developing improved techniques, primarily. for the lKARUS system. This includes two algorithms which allow a Bezier cubic description, two for a general conic representation and, yet another, two for the parabolic case. In addition, a number of algorithms are presented which promote conversions between these mathematical forms; for example, Bezier cubics to a general conic form. Furthennore, algorithms are developed to assist the process of rasterising both cubic and quadratic arcs. Description: This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.

1991-01-01T00:00:00Z Witty, Robert W http://bura.brunel.ac.uk/handle/2438/7395 2013-04-29T09:22:06Z 1981-01-01T00:00:00Z

Title: Small scale software engineering Authors: Witty, Robert W Abstract: In computing, the Software Crisis has arisen because software projects cannot meet their planned timescales, functional capabilities, reliability levels and budgets. This thesis reduces the general problem down to the Small Scale Software Engineering goal of improving the quality and tractability of the designs of individual programs. It is demonstrated that the application of eight abstractions (set, sequence, hierarchy, h-reduction, integration, induction, enumeration, generation) can lead to a reduction in the size and complexity of and an increase in the quality of software designs when expressed via Dimensional Design, a new representational technique which uses the three spatial dimensions to represent set, sequence and hierarchy, whilst special symbols and axioms encode the other abstractions. Dimensional Designs are trees of symbols whose edges perceptually encode the relationships between the nodal symbols. They are easy to draw and manipulate both manually and mechanically. Details are given of real software projects already undertaken using Dimensional Design. Its tool kit, DD/ROOTS, produces high quality, machine drawn, detailed design documentation plus novel quality control information. A run time monitor records and animates execution, measures CPU time and takes snapshots etc; all these results are represented according to Dimensional Design principles to maintain conceptual integrity with the design. These techniques are illustrated by the development of a non-trivial example program. Dimensional Design is axiomatised, compared to existing techniques and evaluated against the stated problem. It has advantages over existing techniques, mainly its clarity of expression and ease of manipulation of individual abstractions due to its graphical basis. Description: This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.

1981-01-01T00:00:00Z Cinar, Zeynep Aysun http://bura.brunel.ac.uk/handle/2438/7391 2013-04-26T15:00:56Z 1999-01-01T00:00:00Z

Title: Numerical modelling of dynamical systems in isothermal chemical reactions and morphogenesis Authors: Cinar, Zeynep Aysun Abstract: Mathematical models of isothermal chemical systems in reactor problems and Turing's theory of morphogenesis with an application in sea-shell patterning are studied. The reaction-diffusion systems describing these models are solved numerically. First- and second-order difference schemes are developed, which are economical and reliable in comparison to classical numerical methods. The linearization process decouples the reaction-diffusion equations thereby allowing the use of different time steps for each differential equation, which may be large due to the excellent stability properties of the methods. The methods avoid having to solve a non-linear algebraic system at each time step. The schemes are suitable for implementation on a parallel machine. Description: This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.

1999-01-01T00:00:00Z