Computational and Analytical Models of Gene Regulations in E. Coli
The project aim is to develop computational and analytical models of gene regulation in E. Coli and thus provide a foundation for analysing the dynamical behaviour of such systems. Cellular processes tend to show very different time scales and display dynamical behaviour ranging from stable steady states, bi- and multistability, to oscillations. Modelling such behaviour thus need to incorporate the stochastic properties of the systems and yet be effective computationally. Moreover, modelling cellular transportation processes incorporates diffusion both in cytoplasm (3D) and by sliding on internal structures like DNA (1D). The regulations collectively form a large regulatory network consisting of thousands of proteins and their interaction with the DNA.
A. Grönlund, P. Lötstedt, and J. Elf, Costs and constraints from time-delayed feedback in small gene regulatory motifs, Proceedings of the National Academy of Sciences, 107 (2010), pp. 8171-8176.