Synchronisation of stochastic oscillators in biochemical systems

A formalism is developed which describes the extent to which stochastic oscillations in biochemical models are synchronised. It is based on the calculation of the complex coherence function within the linear noise approximation. The method is illustrated on a simple example and then applied to study the synchronisation of chemical concentrations in social amoeba. The degree to which variation of rate constants in different cells and the volume of the cells affects synchronisation of the oscillations is explored, and the phase lag calculated. In all cases the analytical results are shown to be in good agreement with those obtained through numerical simulations

Phase lag in epidemics on a network of cities

We study the synchronisation and phase-lag of fluctuations in the number of infected individuals in a network of cities between which individuals commute. The frequency and amplitude of these oscillations is known to be very well captured by the van Kampen system-size expansion, and we use this approximation to compute the complex coherence function that describes their correlation. We find that, if the infection rate differs from city to city and the coupling between them is not too strong, these oscillations are synchronised with a well defined phase lag between cities. The analytic description of the effect is shown to be in good agreement with the results of stochastic simulations for realistic population sizes.Comment: 10 pages, 6 figure

Statistical Mechanics of Recurrent Neural Networks I. Statics

A lecture notes style review of the equilibrium statistical mechanics of recurrent neural networks with discrete and continuous neurons (e.g. Ising, coupled-oscillators). To be published in the Handbook of Biological Physics (North-Holland). Accompanied by a similar review (part II) dealing with the dynamics.Comment: 49 pages, LaTe

Overcoming controllability problems with fewest channels between testers

When testing a system that has multiple physically distributed ports/interfaces it is normal to place a tester at each port. Each tester observes only the events at its port and it is known that this can lead to additional controllability problems. While such controllability problems can be overcome by the exchange of external coordination messages between the testers, this requires the deployment of an external network and may thus increase the costs of testing. The problem studied in this paper is finding a minimum number of coordination channels to overcome controllability problems in distributed testing. Three instances of this problem are considered. The first problem is to find a minimum number of channels between testers in order to overcome the controllability problems in a given test sequence to be applied in testing. The second problem is finding a minimal set of channels that allow us to overcome controllability problems in any test sequence that may be selected from the specification of the system under test. The last problem is to find a test sequence that achieves a particular test objective and in doing so allows fewest channels to be used

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

HYPE with stochastic events

The process algebra HYPE was recently proposed as a fine-grained modelling approach for capturing the behaviour of hybrid systems. In the original proposal, each flow or influence affecting a variable is modelled separately and the overall behaviour of the system then emerges as the composition of these flows. The discrete behaviour of the system is captured by instantaneous actions which might be urgent, taking effect as soon as some activation condition is satisfied, or non-urgent meaning that they can tolerate some (unknown) delay before happening. In this paper we refine the notion of non-urgent actions, to make such actions governed by a probability distribution. As a consequence of this we now give HYPE a semantics in terms of Transition-Driven Stochastic Hybrid Automata, which are a subset of a general class of stochastic processes termed Piecewise Deterministic Markov Processes.Comment: In Proceedings QAPL 2011, arXiv:1107.074