Modelling signaling pathways on diverse scales
Date of Issue2017-12-29
Interdisciplinary Graduate School (IGS)
The dynamic behavior of cell is a broad topic covering wide scope of subjects of varying scales and species. According to the great complexity and diversity involved in understanding cellular behavior, it is necessary to combine the experimental observations from different methods and scales to build up a thorough picture. Modeling techniques originating from physics and mathematics have helped to solve puzzles for complex systems over diverse space and time scales, including numerous biological related systems. In this thesis, we aim to apply the theoretical modeling methods to several biological systems scaling from molecular to ecological levels to develop a quantitative understanding of the interaction and dynamics involved in these subjects. On molecular level, we model the tubulin protein dimer as a feedback control system to show the rich dynamics ranging from picoseconds to hundreds of nanoseconds, as well as the sensitivity of such dimer structure on surrounding biophysical environment. Based on the experimental results of bacteria related study, we mainly focus on the quorum sensing pathway analysis to identify the key components and the robust topological motifs of the interaction network. We also analyze the bacterial ecology system of Ace lake of large scale and high complexity by reaction-diffusion theory and figure out the reason of spatial stratification of different bacteria species. With these modeling works, we are able to further both qualitative and quantitative understanding of molecular interactions and large scale observation of cellular behaviors.