UC San Diego

Synthetic and systems biology propose the rational construction and alteration of the molecular networks that govern life processes, with the purpose of understanding how their architecture relates to the emerging dynamics and for the creation of novel functions. This approach is made possible by the tools of modern molecular biology and the quantitative insights of physical sciences. In this context, microfluidic technology has become the tool of choice for our investigations. Our work is greatly motivated by the prominent role that oscillations play in organizing the dynamics of all living things and by the observation of self-organization of bacterial colonies. In Chapter 2 the basic physics of fluid flow and mass transport in microfluidic devices are presented along with several examples of the application of this technology to quantitative biology. In Chapter 3 I discuss a study on the entrainment of biological clocks through the use of a bacterial synthetic oscillator. In Chapter 4 we discuss the construction and characterization of a genetic oscillator that produces group oscillations. Finally, in Chapter 5 we discuss the dynamic mechanical interactions that arise from the spatially constrained growth of bacteria