Dynamics from a predator-prey-quarry-resource-scavenger model

Allochthonous resources can be found in many foodwebs and can influence both the structure and stability of an ecosystem. In order to better understand the role of how allochthonous resources are transferred as quarry from one predator-prey system to another, we propose a predator-prey-quarry-resource-scavenger (PPQRS) model, which is an extension of an existing model for quarry-resource-scavenger (a predator-prey-subsidy (PPS) model). Instead of taking the allochthonous resource input rate as a constant, as has been done in previous theoretical work, we explicitly incorporated the underlying predator-prey relation responsible for the input of quarry. The most profound differences between PPS and PPQRS system are found when the predator-prey system has limit cycles, resulting in a periodic rather than constant influx of quarry (the allochthonous resource) into the scavenger-resource interactions. This suggests that the way in which allochthonous resources are input into a predator-prey system can have a strong influence over the population dynamics. In order to understand the role of seasonality, we incorporated non-autonomous terms and showed that these terms can either stabilize or destabilize the dynamics, depending on the parameter regime. We also considered the influence of spatial motion (via diffusion) by constructing a continuum partial differential equation (PDE) model over space. We determine when such spatial dynamics essentially give the same information as the ordinary differential equation (ODE) system, versus other cases where there are strong spatial differences (such as spatial pattern formation) in the populations. In situations where increasing the carrying capacity in the ODE model drives the amplitude of the oscillations up, we found that a large carrying capacity in the PDE model results in a very small variation in average population size, showing that spatial diffusion is stabilizing for the PPQRS model.     

Traveling wave solutions of a reaction diffusion model for competing pioneer and climax species

Presented is a reaction-diffusion model for the interaction of pioneer and climax species. For certain parameters the system exhibits bistability and traveling wave solutions. Specifically, we show that when the climax species diffuses at a slow rate there are traveling wave solutions which correspond to extinction waves of either the pioneer or climax species. A leading order analysis is used in the one-dimensional spatial case to estimate the wave speed sign that determines which species becomes extinct. Results of these analyses are then compared to numerical simulations of wave front propagation for the model on one and two-dimensional spatial domains. A simple mechanism for harvesting is also introduced.     

Traveling wave solutions in a plant population model with a seed bank

We propose an integro-difference equation model to predict the spatial spread of a plant population with a seed bank. The formulation of the model consists of a nonmonotone convolution integral operator describing the recruitment and seed dispersal and a linear contraction operator addressing the effect of the seed bank. The recursion operator of the model is noncompact, which poses a challenge to establishing the existence of traveling wave solutions. We show that the model has a spreading speed, and prove that the spreading speed can be characterized as the slowest speed of a class of traveling wave solutions by using an asymptotic fixed point theorem. Our numerical simulations show that the seed bank has the stabilizing effect on the spatial patterns of traveling wave solutions.     

A Traveling Wave Model for Invasion by Precursor and Differentiated Cells

We develop and investigate a continuum model for invasion of a domain by cells that migrate, proliferate and differentiate. The model is applicable to neural crest cell invasion in the developing enteric nervous system, but is presented in general terms and is of broader applicability. Two cell populations are identified and modeled explicitly; a population of precursor cells that migrate and proliferate, and a population of differentiated cells derived from the precursors which have impaired migration and proliferation. The equation describing the precursor cells is based on Fisher’s equation with the addition of a carrying-capacity limited differentiation term. Two variations of the proliferation term are considered and compared. For most parameter values, the model admits a traveling wave solution for each population, both traveling at the same speed. The traveling wave solutions are investigated using perturbation analysis, phase plane methods, and numerical techniques. Analytical and numerical results suggest the existence of two wavespeed selection regimes. Regions of the parameter space are characterized according to existence, shape, and speed of traveling wave solutions. Our observations may be used in conjunction with experimental results to identify key parameters determining the invasion speed for a particular biological system. Furthermore, our results may assist experimentalists in identifying the resource that is limiting proliferation of precursor cells.     

Qualitative Analysis of an ODE Model of a Class of Enzymatic Reactions

The present paper analyzes an ODE model of a certain class of (open) enzymatic reactions. This type of model is used, for instance, to describe the interactions between messenger RNAs and microRNAs. It is shown that solutions defined by positive initial conditions are well defined and bounded on \([0, \infty )\) and that the positive octant of \({\mathbb {R}}^3\) is a positively invariant set. We prove further that in this positive octant there exists a unique equilibrium point, which is asymptotically stable and a global attractor for any initial state with positive components; a controllability property is emphasized. We also investigate the qualitative behavior of the QSSA system in the phase plane \({\mathbb {R}}^2\). For this planar system we obtain similar results regarding global stability by using Lyapunov theory, invariant regions and controllability.     

Backward bifurcation and oscillations in a nested immuno-eco-epidemiological model

This paper introduces a novel partial differential equation immuno-eco-epidemiological model of competition in which one species is affected by a disease while another can compete with it directly and by lowering the first species' immune response to the infection, a mode of competition termed stress-induced competition. When the disease is chronic, and the within-host dynamics are rapid, we reduce the partial differential equation model (PDE) to a three-dimensional ordinary differential equation (ODE) model. The ODE model exhibits backward bifurcation and sustained oscillations caused by the stress-induced competition. Furthermore, the ODE model, although not a special case of the PDE model, is useful for detecting backward bifurcation and oscillations in the PDE model. Backward bifurcation related to stress-induced competition allows the second species to persist for values of its invasion number below one. Furthermore, stress-induced competition leads to destabilization of the coexistence equilibrium and sustained oscillations in the PDE model. We suggest that complex systems such as this one may be studied by appropriately designed simple ODE models.     

Two-dimensional model of calcium waves reproduces the patterns observed in Xenopus oocytes.

Biological excitability enables the rapid transmission of physiological signals over distance. Using confocal fluorescence microscopy, we previously reported circular, planar, and spiral waves of Ca2+ in Xenopus laevis oocytes that annihilated one another upon collision. We present experimental evidence that the excitable process underlying wave propagation depends on Ca2+ diffusion and does not require oscillations in inositol (1,4,5)trisphosphate (IP3) concentration. Extending an existing ordinary differential equation (ODE) model of Ca2+ oscillations to two spatial dimensions, we develop a partial differential equation (PDE) model of Ca2+ excitability. The model assumes that cytosolic Ca2+ couples neighboring Ca2+ release sites. This simple PDE model qualitatively reproduces our experimental observations.     

Global dynamics of a reaction and diffusion model for Lyme disease

This paper is devoted to the mathematical analysis of a reaction and diffusion model for Lyme disease. In the case of a bounded spatial habitat, we obtain the global stability of either disease-free or endemic steady state in terms of the basic reproduction number R?. In the case of an unbounded spatial habitat, we establish the existence of the spreading speed of the disease and its coincidence with the minimal wave speed for traveling fronts. Our analytic results show that R? is a threshold value for the global dynamics and that the spreading speed is linearly determinate.     

Traveling wave solutions for a one-dimensional crawling nematode sperm cell model

In this paper, we proved that the one-dimensional crawling nematode sperm cell model proposed by Mogilner and Verzi (2003) supports traveling wave solutions if there is no disassembly of unbundled filaments in the cell. Uniqueness of traveling wave is established under additional assumptions and numerical examples are also given in the paper. Mathematical methods used include dynamical system techniques, implicit function theorem and global bifurcation theory.Revised version: 16 September 2003     

The effect of spatial scale of resistive inhomogeneity on defibrillation of cardiac tissue

Defibrillation of cardiac tissue can be viewed in the context of dynamical systems theory as the attempt to move a dynamical system from the basin of attraction of one attractor (fibrillation) to another (the uniform rest state) by applying a stimulus whose form is physically constrained. Here we give an introduction to the physical mechanism of cardiac defibrillation from this dynamical perspective and examine the role of resistive inhomogeneity on defibrillation efficacy. Using numerical simulations with rotating waves on a one-dimensional periodic ring, we study the role of the spatial scale of resistive inhomogeneity on defibrillation. For a rotating wave on a periodic ring there are three stable attractors, namely the uniform rest state, a wave traveling clockwise and a wave traveling counterclockwise. As a result, the application of a stimulus has the potential for three different outcomes, namely elimination of the wave, phase resetting of the wave, and reversal of the wave. The results presented here show that with resistive inhomogeneities of large spatial scale, all three of these transitions are possible with large amplitude shocks, so that the probability of defibrillation is bounded well below one, independent of stimulus amplitude. On the other hand, resistive inhomogeneities of small spatial scale produce a defibrillation threshold that is qualitatively consistent with that found experimentally, namely the probability of defibrillation success is an increasing function that approaches one for large enough stimulus amplitude. Extending these results to higher dimensions, we describe conditions for successful defibrillation of functional reentry with large scale spatial inhomogeneity, but find that elimination of anatomical reentry is quite difficult. With small spatial scale inhomogeneity, there are no similar restrictions.     

Modeling Spatial Spread of Infectious Diseases with a Fixed Latent Period in a Spatially Continuous Domain

In this paper, with the assumptions that an infectious disease in a population has a fixed latent period and the latent individuals of the population may diffuse, we formulate an SIR model with a simple demographic structure for the population living in a spatially continuous environment. The model is given by a system of reaction-diffusion equations with a discrete delay accounting for the latency and a spatially non-local term caused by the mobility of the individuals during the latent period. We address the existence, uniqueness, and positivity of solution to the initial-value problem for this type of system. Moreover, we investigate the traveling wave fronts of the system and obtain a critical value c ^* which is a lower bound for the wave speed of the traveling wave fronts. Although we can not prove that this value is exactly the minimal wave speed, numeric simulations seem to suggest that it is. Furthermore, the simulations on the PDE model also suggest that the spread speed of the disease indeed coincides with c ^*. We also discuss how the model parameters affect c ^*.     

Two models for competition between age classes

We consider two lumped age-structured models of juvenile against adult competition, one of which is a compartmental ordinary differential equation (ODE) model and one of which is a system of ODEs with delay derived from the McKendrick partial differential equation (PDE) model. Existence and stability of positive equilibria and existence of oscillatory solutions of both models are studied. Using a competition parameter, which measures the intra-specific competition, we investigate the effects of the competitive interactions between juveniles and adults on the dynamics of the population for both models. We find that these effects are different for the two models and discuss the differences from the modeling perspective. The discussion reveals an interesting relation between the length of the maturation period and the vital rates' dependence on the competition parameter.     

Turing instabilities and spatio-temporal chaos in ratio-dependent Holling-Tanner model

In this paper we consider a modified spatiotemporal ecological system originating from the temporal Holling-Tanner model, by incorporating diffusion terms. The original ODE system is studied for the stability of coexisting homogeneous steady-states. The modified PDE system is investigated in detail with both numerical and analytical approaches. Both the Turing and non-Turing patterns are examined for some fixed parametric values and some interesting results have been obtained for the prey and predator populations. Numerical simulation shows that either prey or predator population do not converge to any stationary state at any future time when parameter values are taken in the Turing-Hopf domain. Prey and predator populations exhibit spatiotemporal chaos resulting from temporal oscillation of both the population and spatial instability. With help of numerical simulations we have shown that Turing-Hopf bifurcation leads to onset of spatio-temporal chaos when predator's diffusivity is much higher compared to prey population. Our investigation reveals the fact that Hopf-bifurcation is essential for the onset of spatiotemporal chaos.     

Spreading speeds and traveling waves in competitive recursion systems

This paper is concerned with the spreading speeds and traveling wave solutions of discrete time recursion systems, which describe the spatial propagation mode of two competitive invaders. We first establish the existence of traveling wave solutions when the wave speed is larger than a given threshold. Furthermore, we prove that the threshold is the spreading speed of one species while the spreading speed of the other species is distinctly slower compared to the case when the interspecific competition disappears. Our results also show that the interspecific competition does affect the spread of both species so that the eventual population densities at the coexistence domain are lower than the case when the competition vanishes.     

一个具有年龄结构的单种群离散反应扩散模型的波前解

利用上下解方法研究了一个具有年龄结构的单种群离散反应扩散模型波前解的存在性,并证明了存在具有临界波速的波前解.     

Spreading speed, traveling waves, and minimal domain size in impulsive reaction-diffusion models

How growth, mortality, and dispersal in a species affect the species' spread and persistence constitutes a central problem in spatial ecology. We propose impulsive reaction-diffusion equation models for species with distinct reproductive and dispersal stages. These models can describe a seasonal birth pulse plus nonlinear mortality and dispersal throughout the year. Alternatively, they can describe seasonal harvesting, plus nonlinear birth and mortality as well as dispersal throughout the year. The population dynamics in the seasonal pulse is described by a discrete map that gives the density of the population at the end of a pulse as a possibly nonmonotone function of the density of the population at the beginning of the pulse. The dynamics in the dispersal stage is governed by a nonlinear reaction-diffusion equation in a bounded or unbounded domain. We develop a spatially explicit theoretical framework that links species vital rates (mortality or fecundity) and dispersal characteristics with species' spreading speeds, traveling wave speeds, as well as minimal domain size for species persistence. We provide an explicit formula for the spreading speed in terms of model parameters, and show that the spreading speed can be characterized as the slowest speed of a class of traveling wave solutions. We also give an explicit formula for the minimal domain size using model parameters. Our results show how the diffusion coefficient, and the combination of discrete- and continuous-time growth and mortality determine the spread and persistence dynamics of the population in a wide variety of ecological scenarios. Numerical simulations are presented to demonstrate the theoretical results.     

A mathematical model of the P-glycoprotein pump as a mediator of multidrug resistance

Cells displaying the classic multidrug resistant (MDR) phenotype possess a transmembrane protein (p170 or P-glycoprotein) which can actively extrude cytotoxic agents from the cytoplasm. A mathematical model of this drug efflux pump has been developed. Outward transport is modeled as a facilitated diffusion process. Since energy-dependent efflux of cytotoxic agents requires that ATP also bind to p170, the model includes a dynamic calculation for efflux rate which considers Michaelis-Menten kinetics for both the substrate agent and ATP. The final system consists of one partial differential equation (PDE) for the facilitated diffusion of substrate agents out of the cell a 2×2 ordinary differential equation (ODE) system for the dynamic calculation of the ATP-ADP pool, and a dynamic algebraic calculation of the efflux rate given substrate levels at the interior cell membrane interface and ATP levels in the cell. A stability analysis of the ATP-ADP pool distribution and a simplistic closed form solution of the linearized PDE are included. Numerical simulations are also provided.     

Mathematical Models for Cell Migration with Real-Time Cell Cycle Dynamics

The fluorescent ubiquitination-based cell cycle indicator, also known as FUCCI, allows the visualization of the G1 and S/G2/M cell cycle phases of individual cells. FUCCI consists of two fluorescent probes, so that cells in the G1 phase fluoresce red and cells in the S/G2/M phase fluoresce green. FUCCI reveals real-time information about cell cycle dynamics of individual cells, and can be used to explore how the cell cycle relates to the location of individual cells, local cell density, and different cellular microenvironments. In particular, FUCCI is used in experimental studies examining cell migration, such as malignant invasion and wound healing. Here we present, to our knowledge, new mathematical models that can describe cell migration and cell cycle dynamics as indicated by FUCCI. The fundamental model describes the two cell cycle phases, G1 and S/G2/M, which FUCCI directly labels. The extended model includes a third phase, early S, which FUCCI indirectly labels. We present experimental data from scratch assays using FUCCI-transduced melanoma cells, and show that the predictions of spatial and temporal patterns of cell density in the experiments can be described by the fundamental model. We obtain numerical solutions of both the fundamental and extended models, which can take the form of traveling waves. These solutions are mathematically interesting because they are a combination of moving wavefronts and moving pulses. We derive and confirm a simple analytical expression for the minimum wave speed, as well as exploring how the wave speed depends on the spatial decay rate of the initial condition.     

Spatial stability of traveling wave solutions of a nerve conduction equation.

A simplified FitzHugh-Nagumo nerve conduction equation with known traveling wave solutions is considered. The spatial stability of these solutions is analyzed to determine which solutions should occur in signal transmission along such a nerve model. It is found that the slower of the two pulse solutions is unstable while the faster one is stable, so the faster one should occur. This agrees with conjectures which have been made about the solutions of other nerve conduction equations. Furthermore for certain parameter values the equation has two periodic wave solutions, each representing a train of impulses, at each frequency less than a maximum frequency wmax. The slower one is found to be unstable and the faster one to be stable, while that at wmax is found to be neutrally stable. These spatial stability results complement the previous results of Rinzel and Keller (1973. Biophys. J. 13: 1313) on temporal stability, which are applicable to the solutions of initial value problems.     

Estimating a predator-prey dynamical model with the parameter cascades method

Summary .   Ordinary differential equations (ODEs) are widely used in ecology to describe the dynamical behavior of systems of interacting populations. However, systems of ODEs rarely provide quantitative solutions that are close to real field observations or experimental data because natural systems are subject to environmental and demographic noise and ecologists are often uncertain about the correct parameterization. In this article we introduce "parameter cascades" as an improved method to estimate ODE parameters such that the corresponding ODE solutions fit the real data well. This method is based on the modified penalized smoothing with the penalty defined by ODEs and a generalization of profiled estimation, which leads to fast estimation and good precision for ODE parameters from noisy data. This method is applied to a set of ODEs originally developed to describe an experimental predator–prey system that undergoes oscillatory dynamics. The new parameterization considerably improves the fit of the ODE model to the experimental data sets. At the same time, our method reveals that important structural assumptions that underlie the original ODE model are essentially correct. The mathematical formulations of the two nonlinear interaction terms (functional responses) that link the ODEs in the predator–prey model are validated by estimating the functional responses nonparametrically from the real data. We suggest two major applications of "parameter cascades" to ecological modeling: It can be used to estimate parameters when original data are noisy, missing, or when no reliable priori estimates are available; it can help to validate the structural soundness of the mathematical modeling approach.