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Wednesday, May 27, 2009
1:30 PM - 2:30 PM
CNLS Conference Room (TA-3, Bldg 1690)

Seminar

A System Design Space for Biochemical Systems: Qualitative Phenotypes and Algebraic Geometry

Michael Saveageau
University of California, Davis

Determining quality of performance for a biological system is critical to identifying and elucidation its design principles. This important task is greatly facilitated by enumeration of regions within the system's design space that exhibit qualitatively distinct phenotypes. First, I will review a few examples of design spaces that have proved useful in revealing design principles for elementary gene circuits. Second, I will present an approach to the generic construction of design spaces. This approach is grounded in the power-law equations that characterize traditional chemical kinetics and, by transformation, the rational functions that characterize biochemical kinetics. In steady state, the analysis of these equations can be reduced to that of linear algebraic equations. Third, these methods will be illustrated with applications from common classes of biochemical network motifs, including unbranched pathways, branched pathways, moiety-transfer cycles, and elementary gene circuits. Finally, in the case of moiety-transfer cycles, predictions will be tested with experimental data from human erythrocytes.

Host: Robert Ecke, CNLS