Reaction network analysis in biochemical signaling pathways

Abstract

The aim of this thesis is to improve the understanding of signaling pathways through a theoretical study of chemical reaction networks. The equilibirum solution to the equations derived from chemical networks will be analytically resolved using tools from algebraic geometry. The chapters are organized as follows: 1. An introduction to chemical dynamics in biological systems with a special emphasis on steady state analysis 2. Complete description of the chemical reaction network theory explaining the new results applied in this thesis We also cover the inverse problem in reaction kinetics whereby if the differential equations could be derived from a chemical system, there is the possibility to apply the theorems covered in the chapter 3. Signaling pathways are constituted by signaling motifs. In this chapter some of the most common motifs are resolved 4. Apoptosis or programmed cell death displays an interesting dynamical mark: bistability, thoroughly analyzed 5. A mathematical model for the JAK-STAT signaling pathway 6. A state of the art discussion of systems biology and autoimmune diseases 7. General conclusions and outlook of this work.