Autonomous resolution based on DNA strand displacement

Authors:
Alfonso Rodríguez-Patón;Iñaki Sainz De Murieta;Petr Sosík
Affiliations:
Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Madrid, Spain;Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Madrid, Spain;Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Madrid, Spain and Institute of Computer Science, Silesian University, Opava, Czech Republic
Venue:
DNA'11 Proceedings of the 17th international conference on DNA computing and molecular programming
Year:
2011

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Abstract

We present a computing model based on the technique of DNA strand displacement which performs a chain of logical resolutions with logical formulae in conjunctive normal form. The model is enzymefree and autonomous. Each clause of a formula is encoded in a separate DNA molecule: propositions are encoded assigning a strand to each proposition p, and its complementary strand to the proposition ¬p; clauses are encoded comprising different propositions in the same strand. The model allows to run logic programs composed of Horn clauses by cascading resolution steps and, therefore, possibly function as an autonomous programmable nano-device. This technique can be also used to solve SAT. The resulting SAT algorithm has a linear time complexity in the number of resolution steps, whereas its spatial complexity is exponential in the number of variables of the formula.