The work presents the analysis of the free boundary value problem related to the one-dimensional invasion model of new species in biofilm reactors. In the framework of continuum approach to mathematical modelling of biofilm growth, the problem consists of a system of non-linear hyperbolic partial differential equations governing the microbial species growth and a system of semi-linear elliptic partial differential equations describing the substrate trends. The model is completed with a system of elliptic partial differential equations governing the diffusion and reaction of planktonic cells, which are able to switch their mode of growth from planktonic to sessile when specific environmental conditions are found. Two systems of non-linear differential equations for the substrate and planktonic cells mass balance within the bulk liquid are also considered. The free boundary evolution is governed by a differential equation that accounts for detachment. The qualitative analysis is performed and a uniqueness and existence result is presented. Furthermore, two special models of biological and engineering interest are discussed numerically. The invasion of Anammox bacteria in a constituted biofilm inhabiting the deammonification units of the wastewater treatment plants is simulated. Numerical simulations are run to evaluate the influence of the colonization process on biofilm structure and activity.

We present the numerical solution of two-point boundary value problems for a third-order linear PDE, representing a linear evolution in one space dimension. To our knowledge, the numerical evaluation of the solution so far could only be obtained by a time-stepping scheme, that must also take into account the issue, generically non-trivial, of the imposition of the boundary conditions. Instead of computing the evolution numerically, we evaluate the novel solution representation formula obtained by the unified transform, also known as Fokas transform. This representation involves complex line integrals, but in order to evaluate these integrals numerically, it is necessary to deform the integration contours using appropriate deformation mappings. We formulate a strategy to implement effectively this deformation, which allows us to obtain accurate numerical results.

We derive a macroscopic model for biofilm formation in a porous medium reactor to investigate the role of suspended bacteria on reactor performance. The starting point is the mesoscopic one-dimensional Wanner–Gujer biofilm model. The following processes are included: hydrodynamics and transport of substrate in the reactor, biofilm and suspended bacteria growth in the pore space, attachment of suspended cells to the biofilm, and detachment of biofilm cells. The mesoscopic equations are up-scaled from the biofilm scale to the reactor scale, yielding a stiff system of balance laws, which we study numerically. We find that suspended bacteria and attachment can have a significant effect on biofilm reactor performance.

Collision of equilibria with a splitting manifold has been locally studied, but might also be a contributing factor to global bifurcations. In particular, a boundary collision can be coincident with collision of a virtual equilibrium with a periodic orbit, giving an analogue to a homoclinic bifurcation. This type of bifurcation is demonstrated in a non-smooth climate application. Here, we describe the non-smooth bifurcation structure, as well as the smooth bifurcation structure for which the non-smooth homoclinic bifurcation is a limiting case.

Biofilms are communities of bacteria that exhibit a multitude of multiscale biomechanical behaviours. Recent experimental advances have led to characterisations of these behaviours in terms of measurements of the viscoelastic moduli of biofilms grown in bioreactors and the fracture and fragmentation properties of biofilms. These properties are macroscale features of biofilms; however, a previous work by our group has shown that heterogeneous microscale features are critical in predicting biofilm rheology. In this paper, we use tools from statistical physics to develop a generative statistical model of the positions of bacteria in biofilms. Specifically, the model is a type of pairwise interaction model (PIM). We show through simulation that the macroscopic mechanical properties of biofilms depend on the choice of microscale spatial model. A key finding is that uniform and non-uniform sets of points lead to differing mechanical properties. This distinction appears not to have been previously considered in mathematical biofilm literature. We also found that realisations of a biologically informed PIM have realistic in silico mechanical properties, and have statistical properties that closely match experimental data. We also note that a Poisson spatial point process of suitable number density also yields realistic mechanical properties, but that the spatial distribution of points does not reflect those occurring in our experimentally observed biofilm.

The asymptotic phase θ of an initial point x in the stable manifold of a limit cycle (LC) identifies the phase of the point on the LC to which the flow φt(x) converges as t → ∞. The infinitesimal phase response curve (iPRC) quantifies the change in timing due to a small perturbation of a LC trajectory. For a stable LC in a smooth dynamical system, the iPRC is the gradient ∇x(θ) of the phase function, which can be obtained via the adjoint of the variational equation. For systems with discontinuous dynamics, the standard approach to obtaining the iPRC fails. We derive a formula for the iPRCs of LCs occurring in piecewise smooth (Filippov) dynamical systems of arbitrary dimension, subject to a transverse flow condition. Discontinuous jumps in the iPRC can occur at the boundaries separating subdomains, and are captured by a linear matching condition. The matching matrix, M, can be derived from the saltation matrix arising in the associated variational problem. For the special case of linear dynamics away from switching boundaries, we obtain an explicit expression for the iPRC. We present examples from cell biology (Glass networks) and neuroscience (central pattern generator models). We apply the iPRCs obtained to study synchronization and phase-locking in piecewise smooth LC systems in which synchronization arises solely due to the crossing of switching manifolds.

In this article, we study the higher-order Moreau's sweeping process introduced in [1], in the case where an exogenous time-varying function u(·) is present in both the linear dynamics and in the unilateral constraints. First, we show that the well-posedness results (existence and uniqueness of solutions) obtained in [1] for the autonomous case, extend to the non-autonomous case when u(·) is smooth and piece-wise analytic, after a suitable state transformation is done. Stability issues are discussed. The complexity of such non-smooth non-autonomous dynamical systems is illustrated in a particular case named the higher-order bouncing ball, where trajectories with accumulations of jumps are exhibited. Examples from mechanics and circuits illustrate some of the results. The link with complementarity dynamical systems and with switching differential-algebraic equations is made.