Data sources and computational approaches for generating models of gene regulatory networks

[No abstract available

Oscillations of the p53-Akt network: Implications on cell survival and death

10.1371/journal.pone.0004407PLoS ONE42e440

Non-linear protocell models: synchronization and chaos

We consider generic protocells models allowing linear and non-linear kinetics for the main involved chemical reactions. We are interested in understanding if and how the protocell division and the metabolism do synchronise to give rise to sustainable evolution of the protocell. Copyright EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2010

A definition of cellular interface problems

We define a class of cellular interface problems (short: CIP) that mathematically model the exchange of molecules in a compartmentalised living cell. Defining and eventually solving such compartmental problems is important for several reasons. They are needed to understand the organisation of life itself, for example by exploring different 'origin of life' hypothesis based on simple metabolic pathways and their necessary division into one or more compartments. In more complex forms investigating cellular interface problems is a way to understand cellular homeostasis of different types, for example ionic fluxes and their composition between all different cellular compartments. Understanding homeostasis and its collapse is important for many physiological medical applications. This class of models is also necessary to formulate efficiently and in detail complex signalling processes taking place in different cell types, with eukaryotic cells the most complex ones in terms of sophisticated compartmentalisation. We will compare such mathematical models of signalling pathways with rule-based models as formulated in membrane computing in a final discussion. The latter is a theory that investigates computer programmes with the help of biological concepts, like a subroutine exchanging data with the environment, in this case a programme with its global variables