Tuesday, February 17, 2015

Spring Course : EE 546 Biomolecular Systems

Biomolecular Systems
EE 546 Advanced Topics in Control System Theory

MW 9:00 - 10:20
EEB 042
Prof. Eric Klavins

This course is an introduction to the principles and tools for modeling, analyzing, and synthesizing the dynamic behavior of synthetic biomolecular systems. We begin with modeling tools such as reaction-rate equations, stochastic models, and specific models of core processes such as transcription, translation, protein-protein interactions, and metabolic networks. We will also consider alternative modeling techniques such as process algebras, Petri nets, and Boolean networks. We will then describe in detail the control and dynamical systems tools used to analyze these models, including stability of equilibria, limit cycles, robustness, parameter uncertainty, and model reduction through time-scale separation. These tools will be applied to design examples from both natural systems and synthetic biomolecular circuits. We address the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and design techniques for ensuring modular behavior. We consider design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. We will use a variety of software including packages for MATLAB and/or Mathematica.

Prerequisites: The course is intended for advanced undergraduates and graduate students. A background in differential equations is a must. Some background in synthetic biology preferred. 

For EE graduate students: EE546 counts as a depth course for SCR students, and as a breath course for other students.

For non-EE students: Check with your graduate advisor. You may be able to have this course count toward your graduate coursework.