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

A two-component phenomenology for homogeneous magnetohydrodynamic turbulence

A one-point closure model for energy decay in three-dimensional magnetohydrodynamic (MHD) turbulence is developed. The model allows for influence of a large-scale magnetic field that may be of strength sufficient to induce Alfvén wave propagation effects, and takes into account components of turbulence in which either the wave-like character is negligible or is dominant. This two-component model evolves energy and characteristic length scales, and may be useful as a simple description of homogeneous MHD turbulent decay. In concert with spatial transport models, it can form the basis for approximate treatment of low-frequency plasma turbulence in a variety of solar, space, and astrophysical contexts