Abstract

The maximum number of strands used is an important measure of a molecular algorithm's complexity. This measure is also called the volume used by the algorithm. Every problem that can be solved by an NP Turing machine with b(n) binary nondeterministic choices can be solved by molecular computation in a polynomial number of steps, with four test tubes, in volume 2 b(n) . We identify a large class of recursive algorithms that can be implemented using bounded nondeterminism. This yields improved molecular algorithms for important problems like 3-SAT, independent set, and 3-colorability. 1. A model of molecular computing Molecular computation was first studied in [1, 20]. The models we define were inspired as well by the work of [3, 28]. A molecular sequence is a string over an alphabet \Sigma (we can use any alphabet we like, encoding characters of \Sigma by finite sequences of base pairs). A test tube is a multiset of molecular sequences. We describe the allowable operations below. Whe...

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