We consider a class of multi-type particle systems whose structure is similar to that of a contact process and show that additivity is equivalent to the existence of a dual process, extending a result of Harris. We prove a necessary and sufficient condition for the model to preserve positive correlations. We then show that complete convergence on Zd holds for a large subclass of models including the two-stage contact process and a household model, and give examples.

We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

Acupuncture has been in clinical practice in China for thousands of years and its analgesia effect is worldwide accepted. However, the mechanism of acupuncture effect is not well understood. The study focus on signaling pathways induced by acupuncture, analyzes the cooperative action of the acupoints’ structure and the associated chemical mediators during acupuncture, establishes a mathematical model clarifying the roadmap of electroneurographic signal startup and transmission mechanism induced by acupuncture, quantitatively analyzing the response in acupoints to acupuncture. These work contribute to reveal the activation and transmission mechanism of neural signals induced by acupuncture from systems biology perspective, lay the foundation for the integration of acupuncture theory and modern science and further guide the clinical treatment and experimental research of acupuncture.

Because of its central role in the global carbon cycle, quantifying the biomass of photosynthetic microalgae in the oceans is crucial to our ability to estimate the oceans’ carbon drawdown. Many traditional methods of primary production assessment have proven to be extremely time consuming and, consequently, have handled only very small sample sizes. The recent advent of in situ bio-optical sensors, such as the water quality monitor (WQM), is now providing lower cost and higher throughput data on these crucial biological communities. These WQMs, however, only quantify the total fluorescence of all individual cells within their optical sample windows, irrespective of size. In this paper, we further develop an established model, based on Pareto random variables, of the size structure of the microalgae community to understand the effect of the WQMs’ sampling and data pooling on their estimates of algal biomass. Unfortunately, evaluating sums of Pareto variables is a notoriously difficult problem. Here, we utilize an approximation for the right-tail of the resulting distribution to derive parameter estimates for the underlying size structure of the microalgae community.

This paper analyses the steady-state operation of a generalized bioreactor model that encompasses a continuous-flow bioreactor and an idealized continuous-flow membrane bioreactor as limiting cases. A biodegradation of organic materials is modelled using Contois growth kinetics. The bioreactor performance is analysed by finding the steady-state solutions of the model and determining their stability as a function of the dimensionless residence time. We show that an effective recycle parameter improves the performance of the bioreactor at moderate values of the dimensionless residence time. However, at sufficiently large values of the dimensionless residence time, the performance of the bioreactor is independent of the recycle ratio.

In this paper, we continue the work started by Steve Krone on the two-stage contact process. We give a simplified proof of the duality relation and answer most of the open questions posed in Krone (1999). We also fill in the details of an incomplete proof.

We provide an introduction to enumerating and constructing invariants of group representations via character methods. The problem is contextualized via two case studies, arising from our recent work: entanglement invariants for characterizing the structure of state spaces for composite quantum systems; and Markov invariants, a robust alternative to parameter-estimation intensive methods of statistical inference in molecular phylogenetics.

Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be nonidentifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. (1998), has been used by many authors in the last few years and is a simple tool to accurately model the changes in allele frequencies in the tree. However, the identifiability of this model has never been proven. Here we prove this model to be identifiable by showing that the model parameters can be expressed as functions of the probability distributions of subsamples, assuming that there are at least two (haploid) individuals sampled from each population. This a step toward proving the consistency of the maximum likelihood estimator of the population tree based on this model.

The paper deals with nonlinear Poisson neuron network models with bounded memory dynamics, which can include both Hebbian learning mechanisms and refractory periods. The state of the network is described by the times elapsed since its neurons fired within the post-synaptic transfer kernel memory span, and the current strengths of synaptic connections, the state spaces of our models being hierarchies of finite-dimensional components. We prove the ergodicity of the stochastic processes describing the behaviour of the networks, establish the existence of continuously differentiable stationary distribution densities (with respect to the Lebesgue measures of corresponding dimensionality) on the components of the state space, and find upper bounds for them. For the density components, we derive a system of differential equations that can be solved in a few simplest cases only. Approaches to approximate computation of the stationary density are discussed. One approach is to reduce the dimensionality of the problem by modifying the network so that each neuron cannot fire if the number of spikes it emitted within the post-synaptic transfer kernel memory span reaches a given threshold. We show that the stationary distribution of this ‘truncated’ network converges to that of the unrestricted network as the threshold increases, and that the convergence is at a superexponential rate. A complementary approach uses discrete Markov chain approximations to the network process.

A version of the contact process (effectively an SIS model) on a finite set of sites is considered in which there is the possibility of spontaneous infection. A companion process is also considered in which spontaneous infection does not occur from the disease-free state. Monotonicity with respect to parameters and initial data is established, and conditions for irreducibility and exponential convergence of the processes are given. For the spontaneous process, a set of approximating equations is derived, and its properties investigated.

Microbial competition for nutrients is a common phenomenon that occurs between species inhabiting the same environment. Bioreactors are often used for the study of microbial competition since the number and type of microbial species can be controlled, and the system can be isolated from other interactions that may occur between the competing species. A common type of competition is the so-called “pure and simple” competition, where the microbial populations interact in no other way except the competition for a single rate-limiting nutrient that affects their growth rates. The issue of whether pure and simple competition under time-invariant conditions can give rise to chaotic behaviour has been unresolved for decades. The third author recently showed, for the first time, that chaos can theoretically occur in these systems by analysing the dynamics of a model where both competing species grow following the biomass-dependent Contois model while the yield coefficients associated with the two species are substrate-dependent. In this paper we show that chaotic behaviour can occur in a much simpler model of pure and simple competition. We examine the case where only one species grows following the Contois model with variable yield coefficient while the other species is allowed to grow following the simple Monod model with constant yield. We show that while the static behaviour of the proposed model is quite simple, the dynamic behaviour is complex and involves period doubling culminating in chaos. The proposed model could serve as a basis to re-examine the importance of Contois kinetics in predicting complex behaviour in microbial competition.

Patchy or divided populations can be important to infectious disease transmission. We first show that Lloyd’s mean crowding index, an index of patchiness from ecology, appears as a term in simple deterministic epidemic models of the SIR type. Using these models, we demonstrate that the rate of movement between patches is crucial for epidemic dynamics. In particular, there is a relationship between epidemic final size and epidemic duration in patchy habitats: controlling inter-patch movement will reduce epidemic duration, but also final size. This suggests that a strategy of quarantining infected areas during the initial phases of a virulent epidemic might reduce epidemic duration, but leave the population vulnerable to future epidemics by inhibiting the development of herd immunity.

A widely used model of carcinogenesis assumes that cells must go through a process of acquiring several mutations before they become cancerous. This implies that at any time there will be several populations of cells at different stages of mutation. In this paper we give exact expressions for the expectations and variances of the number of cells in each stage of such a stochastic multistage cancer model.

This paper concerns a nonlinear doubly degenerate reaction–diffusion equation which appears in a bacterial growth model and is also of considerable mathematical interest. A travelling wave analysis for the equation is carried out. In particular, the qualitative behaviour of both sharp and smooth travelling wave solutions is analysed. This travelling wave behaviour is also verified by some numerical computations for a special case.

Bipartivity is an important network concept that can be applied to nodes, edges and communities. Here we focus on directed networks and look for subnetworks made up of two distinct groups of nodes, connected by ‘one-way’ links. We show that a spectral approach can be used to find hidden substructures of this form. Theoretical support is given for the idealized case where there is limited overlap between subnetworks. Numerical experiments show that the approach is robust to spurious and missing edges. A key application of this work is in the analysis of high-throughput gene expression data, and we give an example where a biologically meaningful directed bipartite subnetwork is found from a cancer microarray dataset.

We present an application of optimal control theory to a simple SIR disease model of avian influenza transmission dynamics in birds. Basic properties of the model, including the epidemic threshold, are obtained. Optimal control theory is adopted to minimize the density of infected birds subject to an appropriate system of ordinary differential equations. We conclude that an optimally controlled seasonal vaccination strategy saves more birds than when there is a low uniform vaccination rate as in resource-limited places.