) Weiping Cai, Anne E. Condon, Robert M. Corn, Elton Glaser, Zhengdong Fei, Tony Frutos, Zhen Guo, Max G. Lagally, Qinghua Liu, Lloyd M. Smith, Andrew Thiel University of Wisconsin Madison, WI 57306 USA Abstract A new model of DNA computation that is based on surface chemistry is studied. Such computations involve the manipulation of DNA strands that are immobilized on a surface, rather than in solution as in the work of Adleman. Surface-based chemistry has been a critical technology in many recent advances in biochemistry and offers several advantages over solution-based chemistry, including simplified handling of samples and elimination of loss of strands, which reduce error in the computation. The main contribution of this paper is in showing that in principle, surface-based DNA chemistry can efficiently support general circuit computation on many inputs in parallel. To do this, an abstract model of computation that allows parallel manipulation of binary inputs is described. It is...