Abstract. The goal of this research is to improve the modular stability and programmability of DNA-based computers and is a second step towards optical programmable DNA computing. The main focus here is on hydrodynamic stability. Clockable microreactors can be connected in various ways to solve combinatorial optimization problems, such as maximum clique or 3-SAT. This work demonstrates by construction how one microreactor design can be programmed to solve any instance of maximum clique up to its given maximum size (N). It reports on an implementation of the architecture proposed previously (McCaskill J S 2001 Biosystems 59 125–38). This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. In this pilot study we are tackling a graph for the maximum clique problem with N ≤ 12, with a special emphasis on N = 6. Furthermore, the design of the DNA solution space will be presented, which is symbolized by a set of bit-strings (words).

Print publication: Issue 5 (October 2002)
Received 3 July 2002, in final form 4 July 2002
Published 20 September 2002