Technology Roadmap for Semiconductors (ITRS) clearly identifies the integration of electrochemical and electrobiological techniques as one of the system-level design challenges that will be faced beyond 2009, when feature sizes shrink below 50nm [5]. Microfluidics-based biochips are soon expected to revolutionize clinical diagnosis, DNA sequencing, and other laboratory procedures involving molecular biology. Most microfluidic biochips are based on the principle of continuous fluid flow and they rely on permanently-etched microchannels, micropumps, and microvalves. We focus here on the automated design of “digital” droplet-based microfluidic biochips. In contrast to continuous-flow systems, digital microfluidics offers dynamic reconfigurability; groups of cells in a microfluidics array can be reconfigured to change their functionality during the concurrent execution of a set of bioassays. We present a simulated annealing-based technique for module placement in such biochips. The pla...