A method for operating a molecular computer solves an NP-complete mathematical problem, that includes obtaining a
molecular sequence encoding an N-SAT problem having a plurality of clauses formed from a plurality of literals in
conjunctive normal form, obtaining replicas of the
molecular sequence, for each pair of replicas, editing the literal-encoding sequences having a variable symbol identifying a particular variable of the N-SAT problem such that, for one replica of the pair, a truth symbol is assigned a
truth value representing true and, for the other replica of the pair, the truth symbol is assigned a
truth value representing false, obtaining, from said editing, a
pool of potential-solution sequences, each potential-solution sequence encoding a potential solution to the N-SAT problem, and identifying, from the
pool of potential-solution sequences, a solution sequence, based on a determination that each encoded clause of a potential-solution sequence contains at least one true-evaluating literal-encoding sequence.