CASAGRANDA , Stefano

This thesis deals with modeling, analysis and reduction of various biological models, with a focus on gene regulatory networks in the bacterium E. coli. Different mathematical approaches are used. In the first part of the thesis, we model, analyze and reduce, using classical tools, a high-dimensional transcription-translation model of RNA...

We present a simple method that allows to analyze the biological processes of a dynamical model and classify them. Along the system trajectories, we decompose the model into biological meaningful processes and then study their activity or inactivity during the time evolution of the system. The structure of the model is then reduced to the core...

Understanding the dynamical behavior of biological networks is complicated due to their large number of components and interactions. We present a simple method to analyse key processes for the system behavior, based on the a priori knowledge of the system trajectory and the simplification of mathematical models of these networks. The method...

Understanding the dynamical behavior of biological networks is complicated due to their large number of components and interactions. We present a method to analyse key processes for the system behavior, based on the a priori knowledge of the system trajectory and the simplification of mathematical models of these networks. The method consists...

Background: Understanding the dynamical behaviour of biological systems is challenged by their large number of components and interactions. While efforts have been made in this direction to reduce model complexity, they often prove insufficient to grasp which and when model processes play a crucial role. Answering these questions is fundamental...

The aim of this paper is to analyze the dynamical behavior of biological models of gene transcription and translation. We focus on a particular positive feedback loop governing the synthesis of RNA polymerase, needed for transcribing its own gene. We write a high-dimension model based on mass-action laws and reduce it to a two-variable model...

The growth of microorganisms involves the conversion of nutrients in the environment into biomass, mostly proteins and other macromolecules. This conversion is accomplished by networks of biochemical reactions cutting across cellular functions, such as metabolism, gene expression, transport and signalling. Mathematical modelling is a powerful...