Patch clamp recordings from ion channels often show periods of repetitive activity, known as bursts, which are noticeably separated from each other by periods of inactivity. Depending on the type of channel, such recordings may exhibit (conductance) levels between the closed (zero) level and the fully open level. Properties of bursts are less subject to problems that arise from recording than are properties for individual sojourns at different levels, and study of bursting behaviour provides important information about the finer structure of the underlying channel gating process. For a general finite state space continuous-time Markov chain model allowing one or more nonzero conductance levels, the present paper establishes results about the semi-Markov structure of a single burst and of a sequence of bursts, and uses this in a unified approach to properties of both theoretical and empirical bursts. The distribution and moments of particular burst properties, including the total charge transfer, the total sojourn time and the total number of visits to specified conductance levels during a burst, are derived. Various extensions are also described.

With the aim of providing greater flexibility in developing and applying shot noise models, this paper studies shot noise on cluster point processes with both pointwise and cluster marks. For example, in financial modelling, responses to events in the financial market may occur in clusters, with random amplitudes including a ‘cluster component’ reflecting a degree of commonness among responses within a cluster. For such shot noise models, general formulae for the characteristic functional are developed and specialized to the case of Neyman-Scott clustering with cluster marks. For several general forms of response function, long range dependence of the corresponding equilibrium shot noise models is investigated. It is shown, for example, that long range dependence holds when the ‘structure component’ of the response function decays slowly enough, or when the response function has a finite random duration with a heavy tailed distribution.

Consider a system of interacting finite Markov chains in continuous time, where each subsystem is aggregated by a common partitioning of the state space. The interaction is assumed to arise from dependence of some of the transition rates for a given subsystem at a specified time on the states of the other subsystems at that time. With two subsystem classes, labelled 0 and 1, the superposition process arising from a system counts the number of subsystems in the latter class. Key structure and results from the theory of aggregated Markov processes are summarized. These are then applied also to superposition processes. In particular, we consider invariant distributions for the level m entry process, marginal and joint distributions for sojourn-times of the superposition process at its various levels, and moments and correlation functions associated with these distributions. The distributions are obtained mainly by using matrix methods, though an approach based on point process methods and conditional probability arguments is outlined. Conditions under which an interacting aggregated Markov chain is reversible are established. The ideas are illustrated with simple examples for which numerical results are obtained using Matlab. Motivation for this study has come from stochastic modelling of the behaviour of ion channels; another application is in reliability modelling.

We study a bivariate stochastic process {X(t)} = Z(t))}, where {XE(t)} is a continuous-time Markov chain describing the environment and {Z(t)} is the process of interest. In the context which motivated this study, {Z(t)} models the gating behaviour of a single ion channel. It is assumed that given {XE(t)}, the channel process {Z(t)} is a continuous-time Markov chain with infinitesimal generator at time t dependent on XE(t), and that the environment process {XE{t)} is not dependent on {Z(t)}. We derive necessary and sufficient conditions for {X(t)} to be time reversible, showing that then its equilibrium distribution has a product form which reflects independence of the state of the environment and the state of the channel. In the special case when the environment controls the speed of the channel process, we derive transition probabilities and sojourn time distributions for {Z(t)} by exploiting connections with Markov reward processes. Some of these results are extended to a stationary environment. Applications to problems arising in modelling multiple ion channel systems are discussed. In particular, we present ways in which a multichannel model in a random environment does and does not exhibit behaviour identical to a corresponding model based on independent and identically distributed channels.

Continuous-time Markov chain models have been widely considered for the gating behaviour of a single ion channel. In such models the state space is usually partitioned into two classes, designated ‘open' and ‘closed', and there is ‘aggregation' in that it is possible to observe only which class the process is in at any given time. Hawkes et al. (1990) have derived an expression for the density function of the exact distribution of an observed open time in such an aggregated Markov model, where brief sojourns in either the open or the closed class are unobservable. This paper extends their result to single ion channel models based on aggregated semi-Markov processes, giving a more direct derivation which is probabilistic and exhibits clearly the combinatorial content.

We consider a semi-Markov process with finite state space, partitioned into two classes termed ‘open' and ‘closed'. It is possible to observe only which class the process is in. We show that complete information concerning the aggregated process is contained in an embedded Markov renewal process, whose parameters, moments and equilibrium behaviour are determined. Such processes have found considerable application in stochastic modelling of single ion channels. In that setting there is time interval omission, i.e. brief sojourns in either class failed to be detected. Complete information on the aggregated process incorporating time interval omission is contained in a Markov renewal process, whose properties are derived, obtained from the above Markov renewal process by a further embedding. The embedded Markov renewal framework is natural, and its invariance to time interval omission leads to considerable economy in the derivation of properties of the observed process. The results are specialised to the case when the underlying process is a continuous-time Markov chain.