The Department of Electrical, Computer & Systems Engineering (ECSE) together with the Center for Automation Technologies and Systems (CATS) present a seminar by Dr. Eric Klavins, Associate Professor of Electrical Engineering at the University of Washington, entitled: "Toward Engineered Collective Behaviors in Bacteria and Yeast," to be held in JEC 3117 on Friday, February 10 at 11:00am. Everyone is welcome!!
The process by which a single cell develops into a multi-celled organism is complicated. A combination of internal logic, control of growth and division, and cell-cell communication must coordinate the behaviors of the growing organism so that it differentiates correctly in time and space, in spite of environmental perturbations, and intrinsic or extrinsic noise. Although several formalisms have been defined to describe development, the relationship between high level programs and the possible biochemical implementation of those programs in micro-organisms is tenuous. Said differently, it is unknown whether the basic mechanisms available to the synthetic biologist are sufficient to implement the pattern formation algorithms defined at higher levels. Here, we introduce a formal specification and programming language, called gro, that allows the programmer to write distributed algorithms at a variety of different levels of abstraction. For example, the programmer may specify that a cell changes from one state to another, of that cell state is defined at the level of a multi-stable gene network with all of the low-copy number noise that would accompany it. The programs can be simulated in an environment that models the basic geometry of micro-colony growth and division, as one might see under a microscope, and also models the production, degradation, and diffusion of signaling molecules. In this talk, we illustrate gro with a variety of examples; focus on the example of symmetry-breaking in particular; and discuss a notion abstraction for gro programs using Wasserstein pseudometrics. The result is a tool that may someday allow the molecular programmer to specify a developmental process at a high level, and refine it, step-by-step, into a low level description of how an implementation would work, and finally to formally compare the specification to an actual experimental implementation.
Eric Klavins is an Associate Professor of Electrical Engineering at the University of Washington in Seattle and holds adjunct appointments in Bioengineering and in Computer Science and Engineering. He received a B.S. in computer science in 1996 from San Francisco State University and a Ph.D. in computer science and engineering in 2001 from the University of Michigan, Ann Arbor. From 2001 to 2003 he was a postdoctoral scholar in the Control and Dynamical Systems Department at the California Institute of Technology. He has been at the University of Washington since 2003. In 2004, he received an NSF CAREER award. His research interests are in synthetic biology, and ranges from design and modeling to experimentation.