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The Robertson model describing a chemical reaction involving three reactants is one of the classical examples of stiffness in ODEs. The stiffness is caused by the occurrence of three reaction rates $k_1,\,k_2$, and $k_3$, with largely differing orders of magnitude, acting as parameters. The model has been widely used as a numerical test problem. Surprisingly, no asymptotic analysis of this multiscale problem seems to exist. In this paper we provide a full asymptotic analysis of the Robertson model under the assumption $k_1, k_3 \ll k_2$. We rewrite the equations as a two-parameter singular perturbation problem in the rescaled small parameters $(\varepsilon_1,\varepsilon_2):=(k_1/k_2,k_3/k_2)$, which we then analyze using geometric singular perturbation theory (GSPT). To deal with the multi-parameter singular structure, we perform blow-ups in parameter- and variable space. We identify four distinct regimes in a neighbourhood of the singular limit \mbox{$(\varepsilon_1,\varepsilon_2)= (0,0)$}. Within these four regimes we use GSPT and additional blow-ups to analyze the dynamics and the structure of solutions. Our asymptotic results are in excellent qualitative and quantitative agreement with the numerics., Comment: 28 pages, 16 figures

We prove the existence of a family of travelling wave solutions in a variant of the $\textit{Zeldovich-Frank-Kamenetskii (ZFK) equation}$, a reaction-diffusion equation which models the propagation of planar laminar premixed flames in combustion theory. Our results are valid in an asymptotic regime which corresponds to a reaction with high activation energy, and provide a rigorous and geometrically informative counterpart to formal asymptotic results that have been obtained for similar problems using $\textit{high activation energy asymptotics}$. We also go beyond the existing results by (i) proving smoothness of the minimum wave speed function $\overline c(\epsilon)$, where $0< \epsilon \ll 1$ is the small parameter, and (ii) providing an asymptotic series for a flat slow manifold which plays a role in the construction of travelling wave solutions for non-minimal wave speeds $c > \overline c(\epsilon)$. The analysis is complicated by the presence of an exponential nonlinearity which leads to two different scaling regimes as $\epsilon \to 0$, which we refer to herein as the $\textit{convective-diffusive}$ and $\textit{diffusive-reactive}$ zones. The main idea of the proof is to use the geometric blow-up method to identify and characterise a $(c,\epsilon)$-family of heteroclinic orbits which traverse both of these regimes, and correspond to travelling waves in the original ZFK equation. More generally, our analysis contributes to a growing number of studies which demonstrate the utility of geometric blow-up approaches to the study dynamical systems with singular exponential nonlinearities., Comment: Accepted version, to appear in SIADS

Any attracting, hyperbolic and proper node of a two-dimensional analytic vector-field has a unique strong-stable manifold. This manifold is analytic. The corresponding weak-stable manifolds are, on the other hand, not unique, but in the nonresonant case there is a unique weak-stable manifold that is analytic. As the system approaches a saddle-node (under parameter variation), a sequence of resonances (of increasing order) occur. In this paper, we give a detailed description of the analytic weak-stable manifolds during this process. In particular, we relate a ``flapping-mechanism'', corresponding to a dramatic change of the position of the analytic weak-stable manifold as the parameter passes through the infinitely many resonances, to the lack of analyticity of the center manifold at the saddle-node. Our work is motivated and inspired by the work of Merle, Rapha\"{e}l, Rodnianski, and Szeftel, where this flapping mechanism is the crucial ingredient in the construction of $C^\infty$-smooth self-similar solutions of the compressible Euler equations.

The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also called dysbiosis, has been correlated with several skin conditions, including acne and atopic dermatitis. Generally, dysbiosis is linked to colonization of the skin by a population of opportunistic pathogenic bacteria. Treatments consisting in non-specific elimination of cutaneous microflora have shown conflicting results. In this article, we introduce a mathematical model based on ordinary differential equations, with 2 types of bacteria populations (skin commensals and opportunistic pathogens) and including the production of antimicrobial peptides to study the mechanisms driving the dominance of one population over the other. By using published experimental data, assumed to correspond to the observation of stable states in our model, we reduce the number of parameters of the model from 13 to 5. We then use a formal specification in quantitative temporal logic to calibrate our model by global parameter optimization and perform sensitivity analyses. On the time scale of 2 days of the experiments, the model predicts that certain changes of the environment, like the elevation of skin surface pH, create favorable conditions for the emergence and colonization of the skin by the opportunistic pathogen population, while the production of human AMPs has non-linear effect on the balance between pathogens and commensals. Surprisingly, simulations on longer time scales reveal that the equilibrium reached around 2 days can in fact be a quasi-stable state followed by the reaching of a reversed stable state after 12 days or more. We analyse the conditions of quasi-stability observed in this model using tropical algebraic methods, and show their non-generic character in contrast to slow-fast systems. These conditions are then generalized to a large class of population dynamics models over any number of species., Comment: arXiv admin note: substantial text overlap with arXiv:2206.10221

In this paper we investigate the stationary profiles of a nonlinear Fokker-Planck equation with small diffusion and nonlinear in- and outflow boundary conditions. We consider corridors with a bottleneck whose width has a global nondegenerate minimum in the interior. In the small diffusion limit the profiles are obtained constructively by using methods from geometric singular perturbation theory (GSPT). We identify three main types of profiles corresponding to: (i) high density in the domain and a boundary layer at the entrance, (ii) low density in the domain and a boundary layer at the exit, and (iii) transitions from high density to low density inside the bottleneck with boundary layers at the entrance and exit. Interestingly, solutions of the last type involve canard solutions generated at the narrowest point of the bottleneck. We obtain a detailed bifurcation diagram of these solutions in terms of the in- and outflow rates. The analytic results based on GSPT are further corroborated by computational experiments investigating corridors with bottlenecks of variable width., Comment: arXiv admin note: text overlap with arXiv:2010.14424

We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial tropical equilibration problem as proxies for symbolic states. The partial tropical equilibration solutions are found algorithmically. These solutions also provide the scaling needed for slow-fast decomposition and model reduction. Any trace of the model can thus be represented as a sequence of local approximations of the full model. We illustrate the method using as case study a biochemical model of the cell cycle., Comment: 23 pages, 5 figures, submitted to CMSB 2022

The qualitative behavior of a recently formulated ODE model for the dynamics of heterogenous aggregates is analyzed. Aggregates contain two types of particles, oligomers and cross-linkers. The motivation is a preparatory step of cellular autophagy, the aggregation of oligomers of the protein p62 in the presence of ubiquitin cross-linkers. A combination of explicit computations, formal asymptotics, and numerical simulations has led to conjectures on the bifurcation behavior, certain aspects of which are proven rigorously in this work. In particular, the stability of the zero state, where the model has a smoothness deficit is analyzed by a combination of regularizing transformations and blow-up techniques. On the other hand, in a different parameter regime, the existence of polynomially growing solutions is shown by Poincar\'e compactification, combined with a singular perturbation analysis .

In this paper, we investigate the stationary profiles of a convection-diffusion model for unidirectional pedestrian flows in domains with a single entrance and exit. The inflow and outflow conditions at both the entrance and exit as well as the shape of the domain have a strong influence on the structure of stationary profiles, in particular on the formation of boundary layers. We are able to relate the location and shape of these layers to the inflow and outflow conditions as well as the shape of the domain using geometric singular perturbation theory. Furthermore, we confirm and exemplify our analytical results by means of computational experiments., Comment: 35 pages

Singular exponential nonlinearities of the form $e^{h(x)\epsilon^{-1}}$ with $\epsilon>0$ small occur in many different applications. These terms have essential singularities for $\epsilon=0$ leading to very different behaviour depending on the sign of $h$. In this paper, we consider two prototypical singularly perturbed oscillators with such exponential nonlinearities. We apply a suitable normalization for both systems such that the $\epsilon\rightarrow 0$ limit is a piecewise smooth system. The convergence to this nonsmooth system is exponential due to the nonlinearities we study. By working on the two model systems we use a blow-up approach to demonstrate that this exponential convergence can be harmless in some cases while in other scenarios it can lead to further degeneracies. For our second model system, we deal with such degeneracies due to exponentially small terms by extending the space dimension, following the approach in Kristiansen [20], and prove - for both systems - existence of (unique) limit cycles by perturbing away from singular cycles having desirable hyperbolicity properties., Comment: 52 pages, 22 figures

A biochemical oscillator model, describing developmental stage of myxobacteria, is analyzed mathematically. Observations from numerical simulations show that in a certain range of parameters, the corresponding system of ordinary differential equations displays stable and robust oscillations. In this work, we use geometric singular perturbation theory and blow-up method to prove the existence of a strongly attracting limit cycle. This cycle corresponds to a relaxation oscillation of an auxiliary system, whose singular perturbation nature originates from the small Michaelis-Menten constants of the biochemical model. In addition, we give a detailed description of the structure of the limit cycle, and the timescales along it., Comment: 38 pages

In this paper, we describe a novel type of relaxation oscillations occurring in a model of substrate-depletion oscillators. Using geometric singular perturbation theory, with blow-up as a key technical tool, we show that the oscillations in this planar model are produced by a complicated interplay between two stable nodes and a discontinuity set in the singular limit $\varepsilon\rightarrow 0$. This interplay produces a new mechanism for producing relaxation-type oscillations, which we also describe in a more general setting.

Micro-Electro Mechanical Systems (MEMS) are defined as very small structures that combine electrical and mechanical components on a common substrate. Here, the electrostatic-elastic case is considered, where an elastic membrane is allowed to deflect above a ground plate under the action of an electric potential, whose strength is proportional to a parameter $\lambda$. Such devices are commonly described by a parabolic partial differential equation that contains a singular nonlinear source term. The singularity in that term corresponds to the so-called "touchdown" phenomenon, where the membrane establishes contact with the ground plate. Touchdown is known to imply the non-existence of steady state solutions and blow-up of solutions in finite time. We study a recently proposed extension of that canonical model, where such singularities are avoided due to the introduction of a regularizing term involving a small "regularization" parameter $\varepsilon$. Methods from dynamical systems and geometric singular perturbation theory, in particular the desingularization technique known as "blow-up", allow for a precise description of steady-state solutions of the regularized model, as well as for a detailed resolution of the resulting bifurcation diagram. The interplay between the two main model parameters $\varepsilon$ and $\lambda$ is emphasized; in particular, the focus is on the singular limit as both parameters tend to zero.

We investigate a singularly perturbed, non-convex variational problem arising in materials science with a combination of geometrical and numerical methods. Our starting point is a work by Stefan M\"uller, where it is proven that the solutions of the variational problem are periodic and exhibit a complicated multi-scale structure. In order to get more insight into the rich solution structure, we transform the corresponding Euler-Lagrange equation into a Hamiltonian system of first order ODEs and then use geometric singular perturbation theory to study its periodic solutions. Based on the geometric analysis we construct an initial periodic orbit to start numerical continuation of periodic orbits with respect to the key parameters. This allows us to observe the influence of the parameters on the behavior of the orbits and to study their interplay in the minimization process. Our results confirm previous analytical results such as the asymptotics of the period of minimizers predicted by M\"uller. Furthermore, we find several new structures in the entire space of admissible periodic orbits.

We study the Olsen model for the peroxidase-oxidase reaction. The dynamics is analyzed using a geometric decomposition based upon multiple time scales. The Olsen model is four-dimensional, not in a standard form required by geometric singular perturbation theory and contains multiple small parameters. These three obstacles are the main challenges we resolve by our analysis. Scaling and the blow-up method are used to identify several subsystems. The results presented here provide a rigorous analysis for two oscillatory modes. In particular, we prove the existence of non-classical relaxation oscillations in two cases. The analysis is based upon desingularization of lines of transcritical and submanifolds of fold singularities in combination with an integrable relaxation phase. In this context our analysis also explains an assumption that has been utilized, based purely on numerical reasoning, in a previous bifurcation analysis by Desroches, Krauskopf and Osinga [{Discret.}{Contin.}{Dyn.}{Syst.}S, 2(4), p.807--827, 2009]. Furthermore, the geometric decomposition we develop forms the basis to prove the existence of mixed-mode and chaotic oscillations in the Olsen model, which will be discussed in more detail in future work., Comment: Submitted version. 46 pages + toc, 9 figures

The Kreiss-Majda Lopatinski determinant encodes a uniform stability property of shock wave solutions to hyperbolic systems of conservation laws in several space variables. This note deals with the Lopatinski determinant for shock waves of sufficiently small amplitude. The determinant is known to be non-zero for so-called extreme shock waves, i. e., shock waves which are asscoiated with either the slowest or the fastest mode the system displays for a given direction of propagation, if the mode is Metivier convex. The result of the note is that for arbitrarily small non-extreme shock waves associated with a Metivier convex mode, the Lopatsinki determinant may vanish.