The effects of symmetry on the dynamics of antigenic variation

In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in malaria, we show how many of the observed dynamical regimes can be explained in terms of the symmetry of interactions between different antigenic variants. The results of this analysis are quite generic, and have wider implications for understanding the dynamics of immune escape of other parasites, as well as for the dynamics of multi-strain diseases.Comment: 21 pages, 4 figures; J. Math. Biol. (2012), Online Firs

Bifurcations of periodic orbits with spatio-temporal symmetries

Motivated by recent analytical and numerical work on two- and three-dimensional convection with imposed spatial periodicity, we analyse three examples of bifurcations from a continuous group orbit of spatio-temporally symmetric periodic solutions of partial differential equations. Our approach is based on centre manifold reduction for maps, and is in the spirit of earlier work by Iooss (1986) on bifurcations of group orbits of spatially symmetric equilibria. Two examples, two-dimensional pulsating waves (PW) and three-dimensional alternating pulsating waves (APW), have discrete spatio-temporal symmetries characterized by the cyclic groups Z_n, n=2 (PW) and n=4 (APW). These symmetries force the Poincare' return map M to be the nth iterate of a map G: M=G^n. The group orbits of PW and APW are generated by translations in the horizontal directions and correspond to a circle and a two-torus, respectively. An instability of pulsating waves can lead to solutions that drift along the group orbit, while bifurcations with Floquet multiplier +1 of alternating pulsating waves do not lead to drifting solutions. The third example we consider, alternating rolls, has the spatio-temporal symmetry of alternating pulsating waves as well as being invariant under reflections in two vertical planes. This leads to the possibility of a doubling of the marginal Floquet multiplier and of bifurcation to two distinct types of drifting solutions. We conclude by proposing a systematic way of analysing steady-state bifurcations of periodic orbits with discrete spatio-temporal symmetries, based on applying the equivariant branching lemma to the irreducible representations of the spatio-temporal symmetry group of the periodic orbit, and on the normal form results of Lamb (1996). This general approach is relevant to other pattern formation problems, and contributes to our understanding of the transition from ordered to disordered behaviour in pattern-forming systems

Analysis of symmetries in models of multi-strain infections

In mathematical studies of the dynamics of multi-strain diseases caused by antigenically diverse pathogens, there is a substantial interest in analytical insights. Using the example of a generic model of multi-strain diseases with cross-immunity between strains, we show that a significant understanding of the stability of steady states and possible dynamical behaviours can be achieved when the symmetry of interactions between strains is taken into account. Techniques of equivariant bifurcation theory allow one to identify the type of possible symmetry-breaking Hopf bifurcation, as well as to classify different periodic solutions in terms of their spatial and temporal symmetries. The approach is also illustrated on other models of multi-strain diseases, where the same methodology provides a systematic understanding of bifurcation scenarios and periodic behaviours. The results of the analysis are quite generic, and have wider implications for understanding the dynamics of a large class of models of multi-strain diseases

Koopman analysis of the long-term evolution in a turbulent convection cell

We analyse the long-time evolution of the three-dimensional flow in a closed cubic turbulent Rayleigh-B\'{e}nard convection cell via a Koopman eigenfunction analysis. A data-driven basis derived from diffusion kernels known in machine learning is employed here to represent a regularized generator of the unitary Koopman group in the sense of a Galerkin approximation. The resulting Koopman eigenfunctions can be grouped into subsets in accordance with the discrete symmetries in a cubic box. In particular, a projection of the velocity field onto the first group of eigenfunctions reveals the four stable large-scale circulation (LSC) states in the convection cell. We recapture the preferential circulation rolls in diagonal corners and the short-term switching through roll states parallel to the side faces which have also been seen in other simulations and experiments. The diagonal macroscopic flow states can last as long as a thousand convective free-fall time units. In addition, we find that specific pairs of Koopman eigenfunctions in the secondary subset obey enhanced oscillatory fluctuations for particular stable diagonal states of the LSC. The corresponding velocity field structures, such as corner vortices and swirls in the midplane, are also discussed via spatiotemporal reconstructions.Comment: 32 pages, 9 figures, article in press at Journal of Fluid Mechanic

Applications of dynamical systems with symmetry

This thesis examines the application of symmetric dynamical systems theory to two areas in applied mathematics: weakly coupled oscillators with symmetry, and bifurcations in flame front equations. After a general introduction in the first chapter, chapter 2 develops a theoretical framework for the study of identical oscillators with arbitrary symmetry group under an assumption of weak coupling. It focusses on networks with 'all to all' Sn coupling. The structure imposed by the symmetry on the phase space for weakly coupled oscillators with Sn, Zn or Dn symmetries is discussed, and the interaction of internal symmetries and network symmetries is shown to cause decoupling under certain conditions. Chapter 3 discusses what this implies for generic dynamical behaviour of coupled oscillator systems, and concentrates on application to small numbers of oscillators (three or four). We find strong restrictions on bifurcations, and structurally stable heteroclinic cycles. Following this, chapter 4 reports on experimental results from electronic oscillator systems and relates it to results in chapter 3. In a forced oscillator system, breakdown of regular motion is observed to occur through break up of tori followed by a symmetric bifurcation of chaotic attractors to fully symmetric chaos. Chapter 5 discusses reduction of a system of identical coupled oscillators to phase equations in a weakly coupled limit, considering them as weakly dissipative Hamiltonian oscillators with very weakly coupling. This provides a derivation of example phase equations discussed in chapter 2. Applications are shown for two van der Pol-Duffing oscillators in the case of a twin-well potential. Finally, we turn our attention to the Kuramoto-Sivashinsky equation. Chapter 6 starts by discussing flame front equations in general, and non-linear models in particular. The Kuramoto-Sivashinsky equation on a rectangular domain with simple boundary conditions is found to be an example of a large class of systems whose linear behaviour gives rise to arbitrarily high order mode interactions. Chapter 7 presents computation of some of these mode interactions using competerised Liapunov-Schmidt reduction onto the kernel of the linearisation, and investigates the bifurcation diagrams in two parameters

Introducing symplectic billiards

In this article we introduce a simple dynamical system called symplectic billiards. As opposed to usual/Birkhoff billiards, where length is the generating function, for symplectic billiards symplectic area is the generating function. We explore basic properties and exhibit several similarities, but also differences of symplectic billiards to Birkhoff billiards.Comment: 41 pages, 16 figure

Compressible magnetoconvection in three dimensions: pattern formation in a strongly stratified layer

The interaction between magnetic fields and convection is interesting both because of its astrophysical importance and because the nonlinear Lorentz force leads to an especially rich variety of behaviour. We present several sets of computational results for magnetoconvection in a square box, with periodic lateral boundary conditions, that show transitions from steady convection with an ordered planform through a regime with intermittent bursts to complicated spatiotemporal behaviour. The constraints imposed by the square lattice are relaxed as the aspect ratio is increased. In wide boxes we find a new regime, in which regions with strong fields are separated from regions with vigorous convection. We show also how considerations of symmetry and associated group theory can be used to explain the nature of these transitions and the sequence in which the relevant bifurcations occur