CDCPreconferenceWorkshop

Full-day CDC 2009 Pre-conference Workshop on Biomolecular Circuit Analysis and Design

Introduction

Systems and Synthetic Biology are two new interdisciplinary research areas that have received a lot of interest in the past years: the first one aims to understand how biological systems function, while the latter considers how such systems can be designed or redesigned for improved or new functionality. To that end, both areas use mathematical modelling and inevitably, tools from control engineering and dynamical systems have found direct and extensive application. At the same time, Systems and Synthetic Biology have driven the development of new control theoretical methods and tools for addressing the complexity and nonlinearity of the models that these disciplines employ. This workshop has three main aims: (1) to present the modelling tools that can be used to describe how biological systems behave at different organizational scales; (2) to review how traditional and new tools which are rooted in systems theory can be used for the analysis of these system descriptions; and (3) to show how such biological networks can be designed and/or redesigned for improved or new functionality both from a theoretical viewpoint and also from a practical one, putting emphasis on the technologies that facilitate this.

Organizers:

• Dr Antonis Papachristodoulou, Department of Engineering Science, University of Oxford.
• Professor Domitilla Del Vecchio, Department of Electrical Engineering and Computer Science, University of Michigan at Ann Arbor.

Additional Speakers:

• Professor Mustafa Khammash, Department of Mechanical Engineering, University of California at Santa Barbara.
• Professor Richard Murray, Control and Dynamical Systems, California Institute of Technology.
• Professor Frank Allgöwer, Institute for Systems Theory and Automatic Control, University of Stuttgart.
• Professor Pablo A. Iglesias, Department of Electrical and Computer Engineering, Johns Hopkins University.

Workshop Goal/Central Theme

The goal of the workshop is provide the participants with a comprehensive review of the various modelling frameworks used in Systems and Synthetic Biology and then present various approaches, rooted in dynamical systems and control theory, for understanding how these systems operate and how they can be designed/redesigned for improved functionality, which is now enabled by technological advances.

The emphasis will be on how tools from dynamical systems and control theory can help answer questions posed by Systems and Synthetic Biology research, but also, how Systems and Synthetic Biology research has driven the development of new theoretical frameworks and tools in dynamical systems and control.

Workshop Content

The following topics will be covered in the workshop:

• Modeling Tools at different organizational scales:
  • Stochastic models: Chemical Master Equation, Chemical Langevin Equation.
  • Deterministic models: Reaction Rate Equations, Michealis-Menten/Hill function dynamics, Chemical Reaction Networks.
• Analysis Tools (Systems Biology):
  • Analysis of stochastic differential equation models.
  • Robust stability of Biological Networks – traditional and new tools. Limit cycles and singular perturbations.
  • Bifurcation Analysis of Biological networks.
• Design Tools (Synthetic Biology):
  • Enabling technologies, design/fabrication examples.
  • Design problems, design and redesign tools/approaches.

Potential Audience

Researchers at different levels interested to engage in systems and synthetic biology research, but also industrial participants who are interested in the potential benefits of systems and synthetic biology research in their field.

Prerequisite

Basic Dynamical Systems and Control Theory – the biological modelling tools will be presented in detail and no background knowledge is required.

Workshop Schedule

Time	Presenter	Topic
8:30-8:45	Professor Domitilla Del Vecchio	Overview of workshop aims and objectives
8:45-9:30	Professor Mustafa Khammash	Stochastic Modelling and Analysis of Biochemical Networks
9:30-10:15	Dr Antonis Papachristodoulou	Modelling biological networks using ordinary differential equations
10:15-10:45	Coffee Break
10:45-11:30	Professor Frank Allgöwer	Robustness and Bifurcation Analysis of biochemical reaction networks
11:30-12:15	Dr Antonis Papachristodoulou	Analysis of biological networks using sum of squares techniques
12:15-13:45	Lunch Break
13:45-14:45	Professor Pablo Iglesias	Control motifs regulating sterol homeostasis
14:45-15:30	Professor Richard Murray	Feedback and Control in Biological Circuit Design
15:30-16:00	Coffee Break
16:00-16:45	Professor Domitilla Del Vecchio	From Retroactivity to Modularity in Bio-molecular Circuit Designs
16:45-17:00	Dr Antonis Papachristodoulou	Wrap-up