Combining Perturbations and Parameter Variation to Influence Mean First Passage Times

Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilibrium number, showing that both competition and predation rates in this model are bifurcating parameters. We then introduce a stochastic process to model the effects of population perturbations. We demonstrate how to evaluate the joint effects of perturbations and drift using the common currency of mean first passage time to transitions between stable states. Our methods and results are quite general, and for example, can relate to issues in both pest control and sustainable harvest. Our results show that parameter drift (1) does not importantly change the expected time to reach target points within a basin of attraction, but (2) can dramatically change the expected time to shift between basins of attraction, through its effects on equilibrium resilience.     

Activity patterns in networks stabilized by background oscillations

The brain operates in a highly oscillatory environment. We investigate here how such an oscillating background can create stable organized behavior in an array of neuro-oscillators that is not observable in the absence of oscillation, much like oscillating the support point of an inverted pendulum can stabilize its up position, which is unstable without the oscillation. We test this idea in an array of electronic circuits coming from neuroengineering: we show how the frequencies of the background oscillation create a partition of the state space into distinct basins of attraction. Thus, background signals can stabilize persistent activity that is otherwise not observable. This suggests that an image, represented as a stable firing pattern which is triggered by a voltage pulse and is sustained in synchrony or resonance with the background oscillation, can persist as a stable behavior long after the initial stimulus is removed. The background oscillations provide energy for organized behavior in the array, and these behaviors are categorized by the basins of attraction determined by the oscillation frequencies. Supported in part by FENA/FCRP Grant No. 0160-G-FD211.     

Multiple Stable Periodic Oscillations in a Mathematical Model of CTL Response to HTLV-I Infection

Stable periodic oscillations have been shown to exist in mathematical models for the CTL response to HTLV-I infection. These periodic oscillations can be the result of mitosis of infected target CD4⁺ cells, of a general form of response function, or of time delays in the CTL response. In this study, we show through a simple mathematical model that time delays in the CTL response process to HTLV-I infection can lead to the coexistence of multiple stable periodic solutions, which differ in amplitude and period, with their own basins of attraction. Our results imply that the dynamic interactions between the CTL immune response and HTLV-I infection are very complex, and that multi-stability in CTL response dynamics can exist in the form of coexisting stable oscillations instead of stable equilibria. Biologically, our findings imply that different routes or initial dosages of the viral infection may lead to quantitatively and qualitatively different outcomes.     

Oscillatory viral dynamics in a delayed HIV pathogenesis model

We consider an HIV pathogenesis model incorporating antiretroviral therapy and HIV replication time. We investigate the existence and stability of equilibria, as well as Hopf bifurcations to sustained oscillations when drug efficacy is less than 100%. We derive sufficient conditions for the global asymptotic stability of the uninfected steady state. We show that time delay has no effect on the local asymptotic stability of the uninfected steady state, but can destabilize the infected steady state, leading to a Hopf bifurcation to periodic solutions in the realistic parameter ranges.     

A food chain ecoepidemic model: Infection at the bottom trophic level

In this paper we consider a three level food web subject to a disease affecting the bottom prey. The resulting dynamics is much richer with respect to the purely demographic model, in that it contains more transcritical bifurcations, gluing together the various equilibria, as well as persistent limit cycles, which are shown to be absent in the classical case. Finally, bistability is discovered among some equilibria, leading to situations in which the computation of their basins of attraction is relevant for the system outcome in terms of its biological implications.     

Alternative (un)stable states in a stochastic predator–prey model

Stochastic models sometimes behave qualitatively differently from their deterministic analogues. We explore the implications of this in ecosystems that shift suddenly from one state to another. This phenomenon is usually studied through deterministic models with multiple stable equilibria under a single set of conditions, with stability defined through linear stability analysis. However, in stochastic systems, some unstable states can trap stochastic dynamics for long intervals, essentially masquerading as additional stable states. Using a predator–prey model, we demonstrate that this effect is sufficient to make a stochastic system with one stable state exhibit the same characteristics as an analogous system with alternative stable states. Although this result is surprising with respect to how stability is defined by standard analyses, we show that it is well-anticipated by an alternative approach based on the system's “quasi-potential.” Broadly, understanding the risk of sudden state shifts will require a more holistic understanding of stability in stochastic systems.     

Pollination ecology and inbreeding depression control individual flowering phenologies and mixed mating

We analyze evolution of individual flowering phenologies by combining an ecological model of pollinator behavior with a genetic model of inbreeding depression for plant viability. The flowering phenology of a plant genotype determines its expected daily floral display which, together with pollinator behavior, governs the population rate of geitonogamous selfing (fertilization among flowers on the same plant). Pollinators select plant phenologies in two ways: they are more likely to visit plants displaying more flowers per day, and they influence geitonogamous selfing and consequent inbreeding depression via their abundance, foraging behavior, and pollen carry‐over among flowers on a plant. Our model predicts two types of equilibria at stable intermediate selfing rates for a wide range of pollinator behaviors and pollen transfer parameters. Edge equilibria occur at maximal or minimal selfing rates and are constrained by pollinators. Internal equilibria occur between edge equilibria and are determined by a trade‐off between pollinator attraction to large floral displays and avoidance of inbreeding depression due to selfing. We conclude that unavoidable geitonogamous selfing generated by pollinator behavior can contribute to the common occurrence of stable mixed mating in plants.     

Global analysis of a two-allele mating system

The global analysis of a two-allele mating system is provided. One allele is dominant to the other. Mating is random, but mating between unlike phenotypes has a lower fertility than that between like phenotypes. The generations are discrete and non-overlapping. The population is considered to be infinite, and the model is deterministic. There are three equilibria of the difference equations. Two of the equilibria are the (two) homozygous states, and these are asymptotically stable. The third equilibrium is polymorphic but is unstable. It is proven that almost all populations converge to one of the two homozygous states. The remaining populations converge to the unstable equilibrium, and lie on a curve that separates the basins of attraction for the other two equilibria. This curve is shown to satisfy some simple properties.     

Consequential classes of resources: Subtle global bifurcation with dramatic ecological consequences in a simple population model

Numerous situations exist in which a consumer uses two different kinds of resources, one fixed, the other renewable, e.g., nesting resources and food resources. With an elementary modification of the basic Lotka-Volterra consumer resource equations, we investigate the population dynamics of a consumer dependent on two resources, one fixed, the other renewable. Emerging from this structure is a situation of alternative attractors that remain qualitatively robust over a significant range of parameter values. However, a dramatic change in basins of attraction is induced by very small changes in parameters due to a global bifurcation. Noteworthy is the fact that the qualitative nature of the alternative equilibria remains constant but the dramatic change in the basins does not arise from subtle differences in initial conditions. Rather, there is a major restructuring of the vector field such that a permanent change involving large sets of initial conditions results from very small changes in parameters.     

Basins of attraction: population dynamics with two stable 4-cycles

We use the concepts of composite maps, basins of attraction, basin switching, and saddle fly-by's to make the ecological hypothesis of the existence of multiple attractors more accessible to experimental scrutiny. Specifically, in a periodically forced insect population growth model we identify multiple attractors, namely, two locally stable 4-cycles. Using the model-predicted basins of attraction, we examine data time series from a Tribolium experiment for evidence of the multiple attractors. We conclude that the multiple attractor hypothesis together with demographic stochasticity accounts for the experimental observations.     

Modeling and analysis of a predator-prey model with disease in the prey

A system of retarded functional differential equations is proposed as a predator-prey model with disease in the prey. Mathematical analyses of the model equations with regard to invariance of non-negativity, boundedness of solutions, nature of equilibria, permanence and global stability are analyzed. If the coefficient in conversing prey into predator k=k(0) is constant (independent of delay tau;, gestation period), we show that positive equilibrium is locally asymptotically stable when time delay tau; is suitable small, while a loss of stability by a Hopf bifurcation can occur as the delay increases. If k=k(0)e(-dtau;) (d is the death rate of predator), numerical simulation suggests that time delay has both destabilizing and stabilizing effects, that is, positive equilibrium, if it exists, will become stable again for large time delay. A concluding discussion is then presented.     

Stochastic Sensitivity Analysis of Noise-Induced Extinction in the Ricker Model with Delay and Allee Effect

A susceptibility of population systems to the random noise is studied on the base of the conceptual Ricker-type model taking into account the delay and Allee effect. This two-dimensional discrete model exhibits the persistence in the form of equilibria, discrete cycles, closed invariant curves, and chaotic attractors. It is shown how the Allee effect constrains the persistence zones with borders defined by crisis bifurcations. We study the role of random noise on the contraction and destruction of these zones. This phenomenon of the noise-induced extinction is investigated with the help of direct numerical simulations and semi-analytical approach based on the stochastic sensitivity functions. Stochastic transitions from the persistence regimes to the extinction are studied by the analysis of the mutual arrangement of the basins of attraction and confidence domains.     

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.     

一类具有时滞和治愈率的HIV病理模型的稳定性

研究一类具有饱和感染率、治愈率和细胞内时滞的HIV病理模型.首先分析平衡态的存在性与稳定性,然后给出染病平衡态对于任意时滞保持稳定（不稳定）的充分条件,并利用Nyquist准则度量染病平衡点保持稳定的时滞长度.     

Evolution Stabilises the Synchronising Dynamics of Poikilotherm Life Cycles

Temperature is the most significant factor controlling developmental timing of most temperate poikilotherms. In the face of climate change, a crucial question is how will poikilothermic organisms evolve when faced with changing thermal environments? In this paper, we integrate models for developmental timing and quantitative genetics. A simple model for determining developmental milestones (emergence times, egg hatch) is introduced, and the general quantitative genetic recursion for the mean value of developmental parameters presented. Evolutionary steps proportional to the difference between current median parameters and parameters currently selected for depend on the fitness, which is assumed to depend on emergence density. Asymptotic states of the joint model are determined, which turn out to be neutrally stable (marginal) fixed points in the developmental model by itself, and an associated stable emergence distribution is also described. An asymptotic convergence analysis is presented for idealized circumstances, indicating basic stability criteria. Numerical studies show that the stability analysis is quite conservative, with basins of attraction to the asymptotic states that are much larger than expected. It is shown that frequency-dependent selection drives oscillatory dynamics and that the asymptotic states balance the asymmetry of the emergence distribution and the fitness function.     

Multiple feedbacks and the prevalence of alternate stable states on coral reefs

The prevalence of alternate stable states on coral reefs has been disputed, although there is universal agreement that many reefs have experienced substantial losses of coral cover. Alternate stable states require a strong positive feedback that causes self-reinforcing runaway change when a threshold is passed. Here we use a simple model of the dynamics of corals, macroalgae and herbivores to illustrate that even weak positive feedbacks that individually cannot lead to alternate stable states can nonetheless do so if they act in concert and reinforce each other. Since the strength of feedbacks varies over time and space, our results imply that we should not reject or accept the general hypothesis that alternate stable states occur in coral reefs. Instead, it is plausible that shifts between alternate stable states can occur sporadically, or on some reefs but not others depending on local conditions. Therefore, we should aim at a better mechanistic understanding of when and why alternate stable states may occur. Our modelling results point to an urgent need to recognize, quantify, and understand feedbacks, and to reorient management interventions to focus more on the mechanisms that cause abrupt transitions between alternate states.     

About deterministic extinction in ratio-dependent predator-prey models

Ratio-dependent predator-prey models set up a challenging issue regarding their dynamics near the origin. This is due to the fact that such models are undefined at (0, 0). We study the analytical behavior at (0, 0) for a common ratio-dependent model and demonstrate that this equilibrium can be either a saddle point or an attractor for certain trajectories. This fact has important implications concerning the global behavior of the model, for example regarding the existence of stable limit cycles. Then, we prove formally, for a general class of ratio-dependent models, that (0, 0) has its own basin of attraction in phase space, even when there exists a non-trivial stable or unstable equilibrium. Therefore, these models have no pathological dynamics on the axes and at the origin, contrary to what has been stated by some authors. Finally, we relate these findings to some published empirical results.     

一类具分段常数变量的捕食-食饵系统的Neimark-Sacker分支

讨论了具时滞与分段常数变量的捕食-食饵生态模型的稳定性及Neimark-Sacker分支;通过计算得到连续模型对应的差分模型,基于特征值理论和Schur-Cohn判据得到正平衡态局部渐进稳定的充分条件;以食饵的内禀增长率为分支参数,运用分支理论和中心流形定理分析了Neimark-Sacker分支的存在性与稳定性条件;通过举例和数值模拟验证了理论的正确性。     

Structured population on two patches: modeling dispersal and delay

We derive from the age-structured model a system of delay differential equations to describe the interaction of spatial dispersal (over two patches) and time delay (arising from the maturation period). Our model analysis shows that varying the immature death rate can alter the behavior of the homogeneous equilibria, leading to transient oscillations around an intermediate equilibrium and complicated dynamics (in the form of the coexistence of possibly stable synchronized periodic oscillations and unstable phase-locked oscillations) near the largest equilibrium.     

Compensation and stability in nonlinear matrix models.

Stability, bifurcation, and dynamic behavior, investigated here in discrete, nonlinear, age-structured models, can be complex; however, restrictions imposed by compensatory mechanisms can limit the behavioral spectrum of a dynamic system. These limitations in transitional behavior of compensatory models are a focal point of this article. Although there is a tendency for compensatory models to be stable, we demonstrate that stability in compensatory systems does not always occur; for example, equilibria arising through a bifurcation can be initially unstable. Results concerning existence and uniqueness of equilibria, stability of the equilibria, and boundedness of solutions suggest that "compensatory" systems might not be compensatory in the literal sense.