Bifurcation analysis of individual-based models in population dynamics

Individual-based models (IBMs) enable us to investigate the effects of inter-individual differences within a population much more easily than traditional modelling approaches based on differential equations. However, the greater flexibility of IBMs makes it difficult to systematically analyse the parameter dependency of the model behaviour so that an IBM may be hard to interpret. In this article, bifurcation analysis techniques for investigating models based on ordinary differential equations (ODE) are transferred to IBMs. For this purpose, we infer stationary solutions of the IBM from the asymptotic dynamics. The stability of these stationary solutions can then be studied depending on model parameters. As shown previously for ODE models (Siekmann et al., 2010; Siekmann, 2013), stationary solutions SiS can be used as bifurcation parameters which allows us to predict survival or extinction of populations by simple algebraic relationships. This is demonstrated with the example of a simple two-strain infection IBM. Moreover, analysing model behaviour based on stationary solutions provides a unified representation of different models that allows us to rigorously compare IBMs with other modelling frameworks like, for example, ODE models. A comparison of the IBM to a population-based ODE model of a two-strain infection leads to similar predictions although both models were built with very different modelling approaches

Coexistence of competitors mediated by nonlinear noise

Stochastic reaction-diffusion equations are a popular modelling approach for studying interacting populations in a heterogeneous environment under the influence of environmental fluctuations. Although the theoretical basis of alternative models such as Fokker- Planck diffusion is not less convincing, movement of populations is most commonly modelled using the diffusion law due to Fick. An interesting feature of Fokker-Planck diffusion is the fact that for spatially varying diffusion coefficients the stationary solution is not a homogeneous distribution – in contrast to Fick’s law of diffusion. Instead, concentration accumulates in regions of low diffusivity and tends to lower levels for areas of high diffusivity. Thus, we may interpret the stationary distribution of the Fokker-Planck diffusion as a reflection of different levels of habitat quality. Moreover, the most common model for environmental fluctuations, linear multiplicative noise, is based on the assumption that individuals respond independently to stochastic environmental fluctuations. For large population densities the assumption of independence is debatable and the model further implies that noise intensities can increase to arbitrarily high levels. Therefore, instead of the commonly used linear multiplicative noise model, we implement environmental variability by an alternative nonlinear noise term which never exceeds a certain maximum noise intensity. With Fokker-Planck diffusion and the nonlinear noise model replacing the classical approaches we investigate a simple invasive system based on the Lotka-Volterra competition model. We observe that the heterogeneous stationary distribution generated by Fokker-Planck diffusion generally facilitates the formation of segregated habitats of resident and invader. However, this segregation can be broken by nonlinear noise leading to coexistence of resident and invader across the whole spatial domain, an effect that would not be possible in the non-spatial version of the competition model for the parameters considered here

Linear oscillations of a compressible hemispherical bubble on a solid substrate

The linear natural and forced oscillations of a hemispherical bubble on a solid substrate are under theoretical consideration. The contact line dynamics is taken into account with the Hocking condition, which eventually leads to interaction of the shape and volume oscillations. Resonant phenomena, mostly pronounced for the bubble with the fixed contact line or with the fixed contact angle, are found out. The limiting case of weakly compressible bubble is studied. The general criterion identifying whether the compressibility of a bubble can be neglected is obtained.Comment: new slightly extended version with some minor changes, added journal reference and DOI information; 12 pages, 8 figures, published in Physics of Fluid

Modelling modal gating of ion channels with hierarchical Markov models

Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately representing activity changes is essential for accurately capturing time course data from ion channels, systematic approaches for modelling modal gating are currently not available. In this paper, we develop a modular approach for building such a model in an iterative process. First, stochastic switching between modes and stochastic opening and closing within modes are represented in separate aggregated Markov models. Second, the continuous-time hierarchical Markov model, a new modelling framework proposed here, then enables us to combine these components so that in the integrated model both mode switching as well as the kinetics within modes are appropriately represented. A mathematical analysis reveals that the behaviour of the hierarchical Markov model naturally depends on the properties of its components. We also demonstrate how a hierarchical Markov model can be parametrized using experimental data and show that it provides a better representation than a previous model of the same dataset. Because evidence is increasing that modal gating reflects underlying molecular properties of the channel protein, it is likely that biophysical processes are better captured by our new approach than in earlier models

Taxis-driven pattern formation in a predator-prey model with group defense

We consider a reaction-diffusion(-taxis) predator-prey system with group defense in the prey. Taxis-driven instability can occur if the group defense influences the taxis rate (Wang et al., 2017). We elaborate that this mechanism is indeed possible but biologically unlikely to be responsible for pattern formation in such a system. Conversely, we show that patterns in excitable media such as spatiotemporal Sierpinski gasket patterns occur in the reaction-diffusion model as well as in the reaction-diffusion-taxis model. If group defense leads to a dome-shaped functional response, these patterns can have a rescue effect on the predator population in an invasion scenario. Preytaxis with prey repulsion at high prey densities can intensify this mechanism leading to taxis-induced persistence. In particular, taxis can increase parameter regimes of successful invasions and decrease minimum introduction areas necessary for a successful invasion. Last, we consider the mean period of the irregular oscillations. As a result of the underlying mechanism of the patterns, this period is two orders of magnitude smaller than the period in the nonspatial system. Counter-intuitively, faster-moving predators lead to lower oscillation periods and eventually to extinction of the predator population. The study does not only provide valuable insights on theoretical spatially explicit predator-prey models with group defense but also comparisons of ecological data with model simulations. © 2020 Elsevier B.V

A type IV functional response with different shapes in a predator-prey model.

Group defense is a phenomenon that occurs in many predator-prey systems. Different functional responses with substantially different properties representing such a mechanism exist. Here, we develop a functional response using timescale separation. A prey-dependent catch rate represents the group defense. The resulting functional response contains a single parameter that controls whether the group defense functional response is saturating or dome-shaped. Based on that, we show that the catch rate must not increase monotonically with increasing prey density to lead to a dome-shaped functional response. We apply bifurcation analysis to show that non-monotonic group defense is usually more successful. However, we also find parameter regions in which a paradox occurs. In this case, higher group defense can give rise to a stable limit cycle, while for lower values, the predator would go extinct. The study does not only provide valuable insight on how to include functional responses representing group defense in mathematical models, but it also clarifies under which circumstances the usage of different functional responses is appropriate

A Stochastic Model of Personality Differences Based on PSI Theory

Personality Systems Interactions (PSI) theory explains differences in personality based on the properties of four cognitive systems—object recognition (OR), intuitive behaviour (IB), intention memory (IM) and extension memory (EM). Each system is associated with characteristic modes of perception and behaviour, so personality is determined by which systems are primarily active. According to PSI theory, the activities of the cognitive systems are regulated by positive and negative affect (reward and punishment). Thus, differences in personality ultimately emerge from four parameters—the sensitivities of up- or downregulating positive and negative affect. The complex interactions of affect and cognitive systems have been represented in a mathematical model based on a system of differential equations. In this study, the environment of a person represented by the mathematical model is modelled by a time series of perturbations with positive and negative affect that are generated by a stochastic process. Comparing the average activities of the cognitive systems for different parameter sets exposed to the same time series of affect perturbations, we observe that different dominant cognitive systems emerge. This demonstrates that different sensitivities for positive and negative affect lead to different modes of cognition and, thus, to different personality types such as agreeable, conscientious, self-determined or independent. Varying the relative frequencies of negative and positive affect perturbations reveals that the average activities of all cognitive systems respond linearly. This observation enables us to predict that conscientious and independent personalities benefit from increased exposure to positive affect, whereas agreeable and self-determined personalities achieve a better balance of their cognitive systems by increased negative affect

Fighting Enemies and Noise: Competition of Residents and Invaders in a Stochastically Fluctuating Environment

The possible control of competitive invasion by infection of the invader and multiplicative noise is studied. The basic model is the Lotka-Volterra competition system with emergent carrying capacities. Several stationary solutions of the non-infected and infected system are identified as well as parameter ranges of bistability. The latter are used for the numerical study of invasion phenomena. The diffusivities, the infection but in particular the white and coloured multiplicative noise are the control parameters. It is shown that not only competition, possible infection and mobilities are important drivers of the invasive dynamics but also the noise and especially its color and the functional response of populations to the emergence of noise

A stochastic model for topographically influenced cell migration.

Migrating cells traverse a range of topographic configurations presented by the native extracellular environment to conduct their physiologic functions. It is well documented cells can modulate their behaviour in response to different topographic features, finding promising applications in biomaterial and bioimplant design. It is useful, in these areas of research, to be able to predict which topographic arrangements could be used to promote certain patterns of migration prior to laboratory experimentation. Despite a profusion of study and interest shown in these fields by experimentalists, the related modelling literature is as yet relatively sparse and tend to focus more on either cell-matrix interaction or morphological responses of cells. We propose a mathematical model for individual cell migration based on an Ornstein-Uhlenbeck process, and set out to see if the model can be used to predict migration patterns on 2-d isotropic and anisotropic topographies, whose characteristics can be broadly described as either uniform flat, uniform linear with variable ridge density or non-uniform disordered with variable feature density. Results suggest the model is capable of producing realistic patterns of migration for flat and linear topographic patterns, with calibrated output closely approximating NIH3T3 fibroblast migration behaviour derived from an experimental dataset, in which migration linearity increased with ridge density and average speed was highest at intermediate ridge densities. Exploratory results for non-uniform disordered topographies suggest cell migration patterns may adopt disorderedness present in the topography and that 'distortion' introduced to linear topographic patterns may not impede linear guidance of migration, given it's magnitude is bounded within certain limits. We conclude that an Ornstein-Uhlenbeck based model for topographically influenced migration may be useful to predict patterns of migration behaviour for certain isotropic (flat) and anisotropic (linear) topographies in the NIH3T3 fibroblast cell line, but additional investigation is required to predict with confidence migration patterns for non-uniform disordered topographic arrangements

Data-Driven Modelling of the Inositol Trisphosphate Receptor (IPR) and its Role in Calcium-Induced Calcium Release (CICR)

We review the current state of the art of data-driven modelling of the inositol trisphosphate receptor (IPR). After explaining that the IPR plays a crucial role as a central regulator in calcium dynamics, several sources of relevant experimental data are introduced. Single ion channels are best studied by recording single-channel currents under different ligand concentrations via the patch-clamp technique. The particular relevance of modal gating, the spontaneous switching between different levels of channel activity that occur even at constant ligand concentrations, is highlighted. In order to investigate the interactions of IPRs, calcium release from small clusters of channels, so-called calcium puffs, can be used. We then present the mathematical framework common to all models based on single-channel data, aggregated continuous-time Markov models, and give a short review of statistical approaches for parameterising these models with experimental data. The process of building a Markov model that integrates various sources of experimental data is illustrated using two recent examples, the model by Ullah et al. and the “Park–Drive” model by Siekmann et al. (Biophys. J. 2012), the only models that account for all sources of data currently available. Finally, it is demonstrated that the essential features of the Park–Drive model in different models of calcium dynamics are preserved after reducing it to a two-state model that only accounts for the switching between the inactive “park” and the active “drive” modes. This highlights the fact that modal gating is the most important mechanism of ligand regulation in the IPR. It also emphasises that data-driven models of ion channels do not necessarily have to lead to detailed models but can be constructed so that relevant data is selected to represent ion channels at the appropriate level of complexity for a given application