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The ability to manipulate and synthesize chemical species on microchip devices provides access to a new and exciting field. These technologies have several advantages throughout the industrial and scientific communities, especially in the emerging areas of biomedical engineering and the life sciences. Recent advances in microscale mixing, reaction, separation, and fluid handling have opened new areas in which process systems engineering techniques can be applied. Here we discuss our initial efforts at creating automatic synthesis methods for the design of microchip-based electrophoretic separation systems that occupy minimal areas. We use piecewise algebraic and logic models to compare the conflicting design goals of maximum system performance and minimum device area. We have implemented both heuristic and numerical optimization design techniques. The long-term goal of our work is the development of methodologies for the design of complete lab-on-a-chip devices.

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