SURF 2012: Effects of circuit "layout" on circuit dynamics

The idea here would be to understand how different design choices (eg, location and direction of genes on a plasmid) affect the dynamics of a circuit. The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. We could do both simulation and experiments (plus comparisons). This would likely involve cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations. More to do here than one person can do, so lots of possibilities.

References:

• http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010
• http://www.sciencemag.org/content/297/5584/1183.full
• http://www.jbioleng.org/content/3/1/4
• http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)