This article was inspired by highly interesting findings related to the stability of DNA double strand. It has been thought that hydrogen bonds between the bases of the two strands are responsible for the stability. This explanation has been challenged (for a popular article see this). According to the article of Bobo Feng et al, the experimental findings support the proposal that hydrophobic forces are actually responsible for the stability. The function of hydrogen bonds would be to take care of correct base pairing rather than stabilization.
In passive state DNA strands would bind together by hydrophobic forces keeping water out of the interior of DNA double strand forming a kind of dry pocket. When DNA is active - say replication or transcription is occurring - an appropriate enzyme opens DNA by splitting the hydrogen bonds and the interior parts get in contact with water. This process requires energy provided by ATP. After than the process could proceed in TGD Universe as discussed here).
The attempt to gain an improved understanding of hydrophobic interactions led to the realization that I have not been considered the possibility that Gibbs free energy might provide a thermodynamical variational principle applicable also to dark matter as heff=n× h0 phases, in particular allowing to get a quantitative grasp on the model of water as a multi-phase system involving magnetic flux tubes with various values of heff(see this).
See the article Minimization of Gibbs free energy as thermodynamical variational principle in TGD framework or the chapter Dark Nuclear Physics and Condensed Matter of "Hyper-finite Factors, p-Adic Length Scale Hypothesis, and Dark Matter Hierarchy: Part II ".
For a summary of earlier postings see Latest progress in TGD.