Intermittent Precipitation-Dependent Interactions, Encompassing Allee Effect, May Yield Vegetation Patterns in a Transitional Parameter Range.

We construct a spatial model that incorporates Allee-type and competition interactions for vegetation as an evolving random field of biomass density. The cumulative effect of close-range precipitation-dependent interactions is controlled by a parameter defining precipitation frequency. We identify a narrow parameter range in which the behavior of the system changes from survival of vegetation to extinction, via a transitional aggregation pattern. The aggregation pattern is tied to the initial configuration and appears to arise differently from Turing's diffusion and differential flow patterns of other models. There is close agreement of our critical transition parameter range with that of the corresponding evolving random mean-field model.

Allee Effects Plus Noise Induce Population Dynamics Resembling Binary Markov Highs and Lows.

We show that the combination of Allee effects and noise can produce a stochastic process with alternating sudden decline to a low population phase, followed, after a random time, by abrupt increase in population density. We introduce a new, flexible, deterministic model of attenuated Allee effects, which interpolates between the logistic and a usual Allee model. Into this model, we incorporate environmental and demographic noise. The solution of the resulting Kolmogorov forward equation shows a dichotomous distribution of residence times with heavy occupation of high, near saturation, and low population states. Investigation of simulated sample paths reveals that indeed attenuated Allee effects and noise, acting together, produce alternating, sustained, low and high population levels. We find that the transition times between the two types of states are approximately exponentially distributed, with different parameters, rendering the embedded hi-low process approximately Markov.

The Relative Contribution of Direct and Environmental Transmission Routes in Stochastic Avian Flu Epidemic Recurrence: An Approximate Analysis.

We present an analysis of an avian flu model that yields insight into the roles of different transmission routes in the recurrence of avian influenza epidemics. Recent modelling work suggests that the outbreak periodicity of the disease is mainly determined by the environmental transmission rate. This conclusion, however, is based on a modelling study that only considers a weak between-host transmission rate. We develop an approximate model for stochastic avian flu epidemics, which allows us to determine the relative contribution of environmental and direct transmission routes to the periodicity and intensity of outbreaks over the full range of plausible parameter values for transmission. Our approximate model reveals that epidemic recurrence is chiefly governed by the product of a rotation and a slowly varying standard Ornstein-Uhlenbeck process (i.e. mean-reverting process). The intrinsic frequency of the damped deterministic version of the system predicts the dominant period of outbreaks. We show that the typical periodicity of major avian flu outbreaks can be explained in terms of either or both types of transmission and that the typical amplitude of epidemics is highly sensitive to the direct transmission rate.

Random fluctuations around a stable limit cycle in a stochastic system with parametric forcing.

Many real populations exhibit stochastic behaviour that appears to have some periodicity. In terms of populations, these time series can occur as limit cycles that arise through seasonal variation of parameters such as, e.g., disease transmission rate. The general mathematical context is that of a stochastic differential system with periodic parametric forcing whose solution is a stochastically perturbed limit cycle. Earlier work identified the power spectral density (PSD) features of these fluctuations by computation of the autocorrelation function of the stochastic process and its transform. Here, we present an alternative analysis which shows that the structure of the fluctuations around the limit cycle is analogous to that of fluctuations about a fixed point. Furthermore, we show that these fluctuations can be expressed, approximately, as a factorization which reveals the combined frequencies of the limit cycle and the stochastic perturbation. This result, based on a new limit theorem near a Hopf point, yields an understanding of the previously found features of the PSD. Further insights are obtained from the corresponding stochastic equations for phase and amplitude.

Moving forward in circles: challenges and opportunities in modelling population cycles.

Population cycling is a widespread phenomenon, observed across a multitude of taxa in both laboratory and natural conditions. Historically, the theory associated with population cycles was tightly linked to pairwise consumer-resource interactions and studied via deterministic models, but current empirical and theoretical research reveals a much richer basis for ecological cycles. Stochasticity and seasonality can modulate or create cyclic behaviour in non-intuitive ways, the high-dimensionality in ecological systems can profoundly influence cycling, and so can demographic structure and eco-evolutionary dynamics. An inclusive theory for population cycles, ranging from ecosystem-level to demographic modelling, grounded in observational or experimental data, is therefore necessary to better understand observed cyclical patterns. In turn, by gaining better insight into the drivers of population cycles, we can begin to understand the causes of cycle gain and loss, how biodiversity interacts with population cycling, and how to effectively manage wildly fluctuating populations, all of which are growing domains of ecological research.

Dynamics of gamma bursts in local field potentials.

In this letter, we provide a stochastic analysis of, and supporting simulation data for, a stochastic model of the generation of gamma bursts in local field potential (LFP) recordings by interacting populations of excitatory and inhibitory neurons. Our interest is in behavior near a fixed point of the stochastic dynamics of the model. We apply a recent limit theorem of stochastic dynamics to probe into details of this local behavior, obtaining several new results. We show that the stochastic model can be written in terms of a rotation multiplied by a two-dimensional standard Ornstein-Uhlenbeck (OU) process. Viewing the rewritten process in terms of phase and amplitude processes, we are able to proceed further in analysis. We demonstrate that gamma bursts arise in the model as excursions of the modulus of the OU process. The associated pair of stochastic phase and amplitude processes satisfies their own pair of stochastic differential equations, which indicates that large phase slips occur between gamma bursts. This behavior is mirrored in LFP data simulated from the original model. These results suggest that the rewritten model is a valid representation of the behavior near the fixed point for a wide class of models of oscillatory neural processes.

The Morris-Lecar neuron model embeds a leaky integrate-and-fire model.

We show that the stochastic Morris-Lecar neuron, in a neighborhood of its stable point, can be approximated by a two-dimensional Ornstein-Uhlenbeck (OU) modulation of a constant circular motion. The associated radial OU process is an example of a leaky integrate-and-fire (LIF) model prior to firing. A new model constructed from a radial OU process together with a simple firing mechanism based on detailed Morris-Lecar firing statistics reproduces the Morris-Lecar Interspike Interval (ISI) distribution, and has the computational advantages of a LIF. The result justifies the large amount of attention paid to the LIF models.

Epidemic highs and lows: a stochastic diffusion model for active cases.

We derive a stochastic epidemic model for the evolving density of infective individuals in a large population. Data shows main features of a typical epidemic consist of low periods interspersed with outbreaks of various intensities and duration. In our stochastic differential model, a novel reproductive term combines a factor expressing the recent notion of 'attenuated Allee effect' and a capacity factor is controlling the size of the process. Simulation of this model produces sample paths of the stochastic density of infectives, which behave much like long-time Covid-19 case data of recent years. Writing the process as a stochastic diffusion allows us to derive its stationary distribution, showing the relative time spent in low levels and in outbursts. Much of the behaviour of the density of infectives can be understood in terms of the interacting drift and diffusion coefficient processes, or, alternatively, in terms of the balance between noise level and the attenuation parameter of the Allee effect. Unexpected results involve the effect of increasing overall noise variance on the density of infectives, in particular on its level-crossing function.

Phase offset determines alpha modulation of gamma phase coherence and hence signal transmission.

We find conditions for optimal phase coherence among sums of phase-offset sine wave pairs of two frequencies, e.g., gamma and alpha. Optimal phase coherence occurs when the respective phase offsets match. Then, using stochastic rate models instead of firing models for both cortical and pulvinar activity, we show that for roughly matching phase offsets of alpha and gamma oscillations there is optimal phase coherence and information transmission between modelled cortical regions.

How sample paths of leaky integrate-and-fire models are influenced by the presence of a firing threshold.

Neural membrane potential data are necessarily conditional on observation being prior to a firing time. In a stochastic leaky integrate-and-fire model, this corresponds to conditioning the process on not crossing a boundary. In the literature, simulation and estimation have almost always been done using unconditioned processes. In this letter, we determine the stochastic differential equations of a diffusion process conditioned to stay below a level S up to a fixed time t(1) and of a diffusion process conditioned to cross the boundary for the first time at t(1). This allows simulation of sample paths and identification of the corresponding mean process. Differences between the mean of free and conditioned processes are illustrated, as well as the role of noise in increasing these differences.

Identification and continuity of the distributions of burst-length and interspike intervals in the stochastic Morris-Lecar neuron.

Using the Morris-Lecar model neuron with a type II parameter set and K(+)-channel noise, we investigate the interspike interval distribution as increasing levels of applied current drive the model through a subcritical Hopf bifurcation. Our goal is to provide a quantitative description of the distributions associated with spiking as a function of applied current. The model generates bursty spiking behavior with sequences of random numbers of spikes (bursts) separated by interburst intervals of random length. This kind of spiking behavior is found in many places in the nervous system, most notably, perhaps, in stuttering inhibitory interneurons in cortex. Here we show several practical and inviting aspects of this model, combining analysis of the stochastic dynamics of the model with estimation based on simulations. We show that the parameter of the exponential tail of the interspike interval distribution is in fact continuous over the entire range of plausible applied current, regardless of the bifurcations in the phase portrait of the model. Further, we show that the spike sequence length, apparently studied for the first time here, has a geometric distribution whose associated parameter is continuous as a function of applied current over the entire input range. Hence, this model is applicable over a much wider range of applied current than has been thought.

Sustained oscillations for density dependent Markov processes.

Simulations of models of epidemics, biochemical systems, and other bio-systems show that when deterministic models yield damped oscillations, stochastic counterparts show sustained oscillations at an amplitude well above the expected noise level. A characterization of damped oscillations in terms of the local linear structure of the associated dynamics is well known, but in general there remains the problem of identifying the stochastic process which is observed in stochastic simulations. Here we show that in a general limiting sense the stochastic path describes a circular motion modulated by a slowly varying Ornstein-Uhlenbeck process. Numerical examples are shown for the Volterra predator-prey model, Sel'kov's model for glycolysis, and a damped linear oscillator.

Plastic systemic inhibition controls amplitude while allowing phase pattern in a stochastic neural field model.

We investigate oscillatory phase pattern formation and amplitude control for a linearized stochastic neuron field model by simulating Mexican-hat-coupled stochastic processes. We find, for several choices of parameters, that spatial pattern formation in the temporal phases of the coupled processes occurs if and only if their amplitudes are allowed to grow unrealistically large. Stimulated by recent work on homeostatic inhibitory plasticity, we introduce static and plastic (adaptive) systemic inhibitory mechanisms to keep the amplitudes stochastically bounded. We find that systems with static inhibition exhibited bounded amplitudes but no sustained phase patterns. With plastic systemic inhibition, on the other hand, the resulting systems exhibit both bounded amplitudes and sustained phase patterns. These results demonstrate that plastic inhibitory mechanisms in neural field models can dynamically control amplitudes while allowing patterns of phase synchronization to develop. Similar mechanisms of plastic systemic inhibition could play a role in regulating oscillatory functioning in the brain.

Impact of Relative Residence Times in Highly Distinct Environments on the Distribution of Heavy Drinkers.

Alcohol consumption is a function of social dynamics, environmental contexts, individuals' preferences and family history. Empirical surveys have focused primarily on identification of risk factors for high-level drinking but have done little to clarify the underlying mechanisms at work. Also, there have been few attempts to apply nonlinear dynamics to the study of these mechanisms and processes at the population level. A simple framework where drinking is modeled as a socially contagious process in low- and high-risk connected environments is introduced. Individuals are classified as light, moderate (assumed mobile), and heavy drinkers. Moderate drinkers provide the link between both environments, that is, they are assumed to be the only individuals drinking in both settings. The focus here is on the effect of moderate drinkers, measured by the proportion of their time spent in "low-" versus "high-" risk drinking environments, on the distribution of drinkers.A simple model within our contact framework predicts that if the relative residence times of moderate drinkers is distributed randomly between low- and high-risk environments then the proportion of heavy drinkers is likely to be higher than expected. However, the full story even in a highly simplified setting is not so simple because "strong" local social mixing tends to increase high-risk drinking on its own. High levels of social interaction between light and moderate drinkers in low-risk environments can diminish the importance of the distribution of relative drinking times on the prevalence of heavy drinking.

Noise sharing and Mexican-hat coupling in a stochastic neural field.

A diffusion-type coupling operator that is biologically significant in neuroscience is a difference of Gaussian functions (Mexican-hat operator) used as a spatial-convolution kernel. We are interested in pattern formation by stochastic neural field equations, a class of space-time stochastic differential-integral equations using the Mexican-hat kernel. We explore quantitatively how the parameters that control the shape of the coupling kernel, the coupling strength, and aspects of spatially smoothed space-time noise influence the pattern in the resulting evolving random field. We confirm that a spatial pattern that is damped in time in a deterministic system may be sustained and amplified by stochasticity. We find that spatially smoothed noise alone causes pattern formation even without direct spatial coupling. Our analysis of the interaction between coupling and noise sharing allows us to determine parameter combinations that are optimal for the formation of spatial pattern.

A stochastic model for water-vegetation systems and the effect of decreasing precipitation on semi-arid environments.

Current climate change trends are affecting the magnitude and recurrence of extreme weather events. In particular, several semi-arid regions around the planet are confronting more intense and prolonged lack of precipitation, slowly transforming part of these regions into deserts in some cases. Although it is documented that a decreasing tendency in precipitation might induce earlier disappearance of vegetation, quantifying the relationship between decrease of precipitation and vegetation endurance remains a challenging task due to the inherent complexities involved in distinct scenarios. In this paper we present a model for precipitation-vegetation dynamics in semi-arid landscapes that can be used to explore numerically the impact of decreasing precipitation trends on appearance of desertification events. The model, a stochastic differential equation approximation derived from a Markov jump process, is used to generate extensive simulations that suggest a relationship between precipitation reduction and the desertification process, which might take several years in some instances.

Constructing 1/omegaalpha noise from reversible Markov chains.

This paper gives sufficient conditions for the output of 1/omegaalpha noise from reversible Markov chains on finite state spaces. We construct several examples exhibiting this behavior in a specified range of frequencies. We apply simple representations of the covariance function and the spectral density in terms of the eigendecomposition of the probability transition matrix. The results extend to hidden Markov chains. We generalize the results for aggregations of AR1-processes of C. W. J. Granger [J. Econometrics 14, 227 (1980)]. Given the eigenvalue function, there is a variety of ways to assign values to the states such that the 1/omegaalpha condition is satisfied. We show that a random walk on a certain state space is complementary to the point process model of 1/omega noise of B. Kaulakys and T. Meskauskas [Phys. Rev. E 58, 7013 (1998)]. Passing to a continuous state space, we construct 1/omegaalpha noise which also has a long memory.

Optimal signal in sensory neurons under an extended rate coding concept.

We define an optimal signal in parametric neuronal models on the basis of interspike interval data and rate coding schema. Under the classical approach the optimal signal is located where the frequency transfer function is steepest. Its position coincides with the inflection point of this curve. This concept is extended here by using Fisher information which is the inverse asymptotic variance of the best estimator and its dependence on the parameter value indicates accuracy of estimation. We compare the signal producing maximal Fisher information with the inflection point of the sigmoidal frequency transfer function.

Soft threshold stochastic resonance.

Soft thresholds are ubiquitous in living organisms, in particular in mechanisms of neurons and of neural networks such as sensory systems. Which soft threshold functions produce (threshold) stochastic resonance remains a question. The answer may depend on the information measure used. We argue that Fisher information about signal parameters is an attractive measure of information transmission across soft thresholds. We illustrate how the pattern of information changes as a signal moves across a soft threshold. For some signals this pattern is much the same whether Fisher information or signal-to-noise ratio is used as a measure of information transmission. Noninvertibility of the threshold function, rather than its steepness, is important for stochastic resonance measured by Fisher information.

The ISI distribution of the stochastic Hodgkin-Huxley neuron.

The simulation of ion-channel noise has an important role in computational neuroscience. In recent years several approximate methods of carrying out this simulation have been published, based on stochastic differential equations, and all giving slightly different results. The obvious, and essential, question is: which method is the most accurate and which is most computationally efficient? Here we make a contribution to the answer. We compare interspike interval histograms from simulated data using four different approximate stochastic differential equation (SDE) models of the stochastic Hodgkin-Huxley neuron, as well as the exact Markov chain model simulated by the Gillespie algorithm. One of the recent SDE models is the same as the Kurtz approximation first published in 1978. All the models considered give similar ISI histograms over a wide range of deterministic and stochastic input. Three features of these histograms are an initial peak, followed by one or more bumps, and then an exponential tail. We explore how these features depend on deterministic input and on level of channel noise, and explain the results using the stochastic dynamics of the model. We conclude with a rough ranking of the four SDE models with respect to the similarity of their ISI histograms to the histogram of the exact Markov chain model.