Models of Life Dynamics and Regulation in Biological Systems

Reflecting the major advances that have been made in the field over the past decade, this book provides an overview of current models of biological systems. The focus is on simple quantitative models, highlighting their role in enhancing our understanding of the strategies of gene regulation and dynamics of information transfer along signalling pathways, as well as in unravelling the interplay between function and evolution. The chapters are self-contained, each describing key methods for studying the quantitative aspects of life through the use of physical models. They focus, in particular, on connecting the dynamics of proteins and DNA with strategic decisions on the larger scale of a living cell, using E. coli and phage lambda as key examples. Encompassing fields such as quantitative molecular biology, systems biology and biophysics, this book will be a valuable tool for students from both biological and physical science backgrounds.

Preface; 1. Life from a physics perspective; 2. E. coli as a model system; 3. Dynamics of regulatory links; 4. Statistical mechanics of phage λ; 5. Diffusion and randomness in transcription; 6. Stochastic genes and persistent decisions; 7. Gene regulation and epigenetics in cis; 8. Feedback circuits; 9. Networks; 10. Signalling and metabolic networks; 11. Agent-based models of signalling and selection; 12. Competition and diversity; 13. Evolution and extinction; Appendix; References; Index.

Kim Sneppen is Professor of Physics at the Niels Bohr Institute and Director of the interdisciplinary Center for Models of Life (CMOL) at Copenhagen University, Denmark. Drawing on experience across several academic disciplines, his work explores the frontier between complex dynamical systems and living systems, and in his role at CMOL he promotes hands-on development of quantitative models of central biological processes. Sneppen is also co-author of Physics in Molecular Biology (Cambridge University Press, 2005).