A Control Theoretic Approach to Designing Biochemical Feedback Circuits
Recent technological advancements have enabled us to construct artificial biochemical networks, or biocircuits, that produce desired dynamic functions such as bistability, oscillations and logic gates by assembling DNA parts. Toward a systematic engineering of complex biological systems, model-based biocircuit design has been increasingly important in recent years. In this talk, we present a control theoretic framework for the systematic design and identification of biocircuits along with experimental results. In the first part of the talk, we introduce a general model representation of biocircuits and provide rigorous theoretical tools for the analysis of biochemical dynamics. The theoretical tools are demonstrated by experimentally designing biochemical oscillator circuits. In the latter half of the talk, we propose a set-based identification method for identifying a set of parameters that all explain time-series experimental data, using a convex relaxation approach. We show, using an existing biocircuit, that the identification method can systematically characterize the uncertainty of parameters. Finally, we discuss how we can integrate the set-based identification method into a robust biocircuit design problem.
Yutaka Hori received B.E., M.I.Sc.T. and Ph.D. degrees in information science and technology from the University of Tokyo in 2008, 2010 and 2013, respectively. In 2010–2011, he was a visiting student at University of California, Santa Barbara. He is currently a JSPS postdoctoral fellow with Prof. Richard Murray at California Institute of Technology. His research interests lie in feedback control theory of networked dynamical systems and synthetic biology. He is a recipient of Annual Conference Young Author’s Award at ICROS-SICE International Joint Conference in 2009 and a Finalist of Best Student Paper Award at IEEE Multi-Conference on Systems and Control in 2010 and Best Paper Award at Asian Control Conference in 2011.
Host: Ashutosh Nayyar