Modeling and Analysis of Cellular Processes with Dynamical Probabilistic P Systems: Questions, Methods and Results

Mathematical modeling and computational methods facilitate the study of the functioning of biological systems and the analysis of their emergent behaviors. According to the nature of the biological system under investigation, to the available experimental data, and to the scientific question for which the model is developed, a proper mathematical formalism needs to be selected. In this work we recapitulate the results we obtained from the analysis of mechanistic models of two signal transduction pathways, outlining the relevance of the use of multi-volume models, when required, in the context of membrane systems. We also summarize some qualitative computational methods—based on the concept of communicating classes of the configurations space of membrane systems— which allow to investigate dynamical features of biological systems without the need to perform simulations. We finally discuss some general issues concerning the modeling and analysis of cellular processes.