This dissertation focuses on the further development of creating accurate numerical models of complex dynamical systems using the holistic discretisation technique [Roberts, Appl. Num. Model., 37:371-396, 2001]. I extend the application from second to fourth order systems and from only one spatial dimension in all previous work to two dimensions (2D). We see that the holistic technique provides useful and accurate numerical discretisations on coarse grids. We explore techniques to model the evolution of spatial patterns governed by pdes such as the Kuramoto-Sivashinsky equation and the real-valued Ginzburg-Landau equation. We aim towards the simulation of fluid flow and convection in three spatial dimensions. I show that significant steps have been taken in this dissertation towards achieving this aim. Holistic discretisation is based upon centre manifold theory [Carr, Applications of centre manifold theory, 1981] so we are assured that the numerical discretisation accurately models the dynamical system and may be constructed systematically. To apply centre manifold theory the domain is divided into elements and using a homotopy in the coupling parameter, subgrid scale fields are constructed consisting of actual solutions of the governing partial differential equation(pde). These subgrid scale fields interact through the introduction of artificial internal boundary conditions. View the centre manifold (macroscale) as the union of all states of the collection of subgrid fields (microscale) over the physical domain. Here we explore how to extend holistic discretisation to the fourth order Kuramoto-Sivashinsky pde. I show that the holistic models give impressive accuracy for reproducing the steady states and time dependent phenomena of the Kuramoto-Sivashinsky equation on coarse grids. The holistic method based on local dynamics compares favourably to the global methods of approximate inertial manifolds. The excellent performance of the holistic models shown here is strong evidence in support of the holistic discretisation technique. For shear dispersion in a 2D channel a one-dimensional numerical approximation is generated directly from the two-dimensional advection-diffusion dynamics. We find that a low order holistic model contains the shear dispersion term of the Taylor model [Taylor, IMA J. Appl. Math., 225:473-477, 1954]. This new approach does not require the assumption of large x scales, formerly absolutely crucial in deriving the Taylor model. I develop holistic discretisation for two spatial dimensions by applying the technique to the real-valued Ginzburg-Landau equation as a representative example of second order pdes. The techniques will apply quite generally to second order reaction-diffusion equations in 2D. This is the first study implementing holistic discretisation in more than one spatial dimension. The previous applications of holistic discretisation have developed algebraic forms of the subgrid field and its evolution. I develop an algorithm for numerical construction of the subgrid field and its evolution for 1D and 2D pdes and explore various alternatives. This new development greatly extends the class of problems that may be discretised by the holistic technique. This is a vital step for the application of the holistic technique to higher spatial dimensions and towards discretising the Navier-Stokes equations.

The thesis is based on using dynamical systems theories and techniques to study the qualitative dynamics of herpes simplex virus type 2 (HSV-2), a sexually-transmitted disease of major public health significance. A deterministic model for the interaction of the virus with the immune system in the body of an infected individual (in vivo) is designed first of all. It is shown, using Lyapunov function and LaSalle's Invariance Principle, that the virus-free equilibrium of the model is globally-asymptotically stable whenever a certain biological threshold, known as the reproduction number, is less than unity. Furthermore, the model has at least one virus-present equilibrium when the threshold quantity exceeds unity. Using persistence theory, it is shown that the virus will always be present in vivo whenever the reproduction threshold exceeds unity. The analyses (theoretical and numerical) of this model show that a future HSV-2 vaccine that enhances cell-mediated immune response will be effective in curtailling HSV-2 burden in vivo. A new single-group model for the spread of HSV-2 in a homogenously-mixed sexually-active population is also designed. The disease-free equilibrium of the model is globally-asymptotically stable when its associated reproduction number is less than unity. The model has a unique endemic equilibrium, which is shown to be globally-stable for a special case, when the reproduction number exceeds unity. The model is extended to incorporate an imperfect vaccine with some therapeutic benefits. Using centre manifold theory, it is shown that the resulting vaccination model undergoes a vaccine-induced backward bifurcation (the epidemiological importance of the phenomenon of backward bifurcation is that the classical requirement of having the reproduction threshold less than unity is, although necessary, no longer sufficient for disease elimination. In such a case, disease elimination depends upon the initial sizes of the sub-populations of the model). Furthermore, it is shown that the use of such an imperfect vaccine could lead to a positive or detrimental population-level impact (depending on the sign of a certain threshold quantity). The model is extended to incorporate the effect of variability in HSV-2 susceptibility due to gender differences. The resulting two-group (sex-structured) model is shown to have essentially the same qualitative dynamics as the single-group model. Furthermore, it is shown that adding periodicity to the corresponding autonomous two-group model does not alter the dynamics of the autonomous two-group model (with respect to the elimination of the disease). The model is used to evaluate the impact of various anti-HSV control strategies. Finally, the two-group model is further extended to address the effect of risk structure (i.e., risk of acquiring or transmitting HSV-2). Unlike the two-group model described above, it is shown that the risk-structured model undergoes backward bifurcation under certain conditions (the backward bifurcation property can be removed if the susceptible population is not stratified according to the risk of acquiring infection). Thus, one of the main findings of this thesis is that risk structure can induce the phenomenon of backward bifurcation in the transmission dynamics of HSV-2 in a population.

The thesis is based on using dynamical systems theories and techniques to study the qualitative dynamics of herpes simplex virus type 2 (HSV-2), a sexually-transmitted disease of major public health significance. A deterministic model for the interaction of the virus with the immune system in the body of an infected individual (in vivo) is designed first of all. It is shown, using Lyapunov function and LaSalle's Invariance Principle, that the virus-free equilibrium of the model is globally-asymptotically stable whenever a certain biological threshold, known as the reproduction number, is less than unity. Furthermore, the model has at least one virus-present equilibrium when the threshold quantity exceeds unity. Using persistence theory, it is shown that the virus will always be present in vivo whenever the reproduction threshold exceeds unity. The analyses (theoretical and numerical) of this model show that a future HSV-2 vaccine that enhances cell-mediated immune response will be effective in curtailling HSV-2 burden in vivo. A new single-group model for the spread of HSV-2 in a homogenously-mixed sexually-active population is also designed. The disease-free equilibrium of the model is globally-asymptotically stable when its associated reproduction number is less than unity. The model has a unique endemic equilibrium, which is shown to be globally-stable for a special case, when the reproduction number exceeds unity. The model is extended to incorporate an imperfect vaccine with some therapeutic benefits. Using centre manifold theory, it is shown that the resulting vaccination model undergoes a vaccine-induced backward bifurcation (the epidemiological importance of the phenomenon of backward bifurcation is that the classical requirement of having the reproduction threshold less than unity is, although necessary, no longer sufficient for disease elimination. In such a case, disease elimination depends upon the initial sizes of the sub-populations of the model). Furthermore, it is shown that the use of such an imperfect vaccine could lead to a positive or detrimental population-level impact (depending on the sign of a certain threshold quantity). The model is extended to incorporate the effect of variability in HSV-2 susceptibility due to gender differences. The resulting two-group (sex-structured) model is shown to have essentially the same qualitative dynamics as the single-group model. Furthermore, it is shown that adding periodicity to the corresponding autonomous two-group model does not alter the dynamics of the autonomous two-group model (with respect to the elimination of the disease). The model is used to evaluate the impact of various anti-HSV control strategies. Finally, the two-group model is further extended to address the effect of risk structure (i.e., risk of acquiring or transmitting HSV-2). Unlike the two-group model described above, it is shown that the risk-structured model undergoes backward bifurcation under certain conditions (the backward bifurcation property can be removed if the susceptible population is not stratified according to the risk of acquiring infection). Thus, one of the main findings of this thesis is that risk structure can induce the phenomenon of backward bifurcation in the transmission dynamics of HSV-2 in a population.