A second complication arises from the initiation energy ΦI that describes the entropy necessary to bring the two molecules into contact. This term, which is considered to be independent of sequence length and composition [47], has to be taken into account exactly once for every dimer structure if and only if the structure contains at least one base pair (i, j) that crosses the cut, i.e., i ≤ n1 <j. The resulting bookkeeping problems fortunately can be avoided by introducing this term only after the dynamic programming tables have been filled. To this end we observe that Zi, j = , 1 ≤ i, j ≤ n1 are the partition functions for subsequences of the isolated A molecule, while , 1 ≤ i, j ≤ n2 are the corresponding quantities for the second interaction partner. Thus we can immediately compute the partition function ZAB - ZAZB that counts only the structures with intermolecular pairs, i.e., those that carry the additional initiation energy contribution. The total partition function including the initiation term is therefore