2026-07-27T10:08:16Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:26779 2026-07-27T07:33:58Z ddc:004 open_access

Thermodynamic Binding Networks Capture Equilibrium Monomer-Polymer Thermodynamics Yilmaz, And Kaan Ata Soloveichik, David Luchsinger, Austin Thermodynamic Binding Networks Thermodynamic Affinity Networks Equilibrium Thermodynamics Thermodynamic Binding Networks (TBNs) are a minimal model for molecular thermodynamics. Despite their simplicity, the stable behavior of these systems can be unexpectedly nontrivial. To better understand the expressive power of the model, we compare TBNs with Thermodynamic Affinity Networks (TANs), a partition-scoring formalism in which polymer-level favorability is specified directly, rather than derived from domain-level interactions. We show that these two models are thermodynamically equivalent at the level of stable configurations: every TBN can be represented directly by a TAN, and every TAN can be indirectly realized by a TBN whose stable configurations map exactly to the stable configurations of the TAN. The key idea in the latter direction is to use auxiliary monomers that allow the system to convert polymer-level free-energy rewards specified by the TAN into entropic gains from separate complexes in the TBN. This correspondence shows that the local rules of TBNs do not limit their equilibrium expressive power nearly as much as one might expect. In this minimum-free-energy sense of equilibrium, TBNs capture the coarse-grained monomer-polymer thermodynamics formalized by TANs. Schloss Dagstuhl – Leibniz-Zentrum für Informatik And Kaan Ata Yilmaz and David Soloveichik and Austin Luchsinger 2026 Is Part Of LIPIcs, Volume 387, 32nd International Conference on DNA Computing and Molecular Programming (DNA 32) (2026) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.32.9 urn:nbn:de:0030-drops-267796 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.32.9 eng https://creativecommons.org/licenses/by/4.0/legalcode