Figure 12.

Irreversible reactions as a consequence of max-helix and reject-remote semantics. (a) Max-helix semantics. Domains b and c are always part of the same max-helix move, domain a can sometimes, but not always be combined with b and c. This competition of different rules can lead to irreversible reactions, e.g. $\{\mathrm{A}34\to \mathrm{A}43,\mathrm{A}34\to \mathrm{A}4\}$. However, note that the every single complex is still part of the same SCC, where every state is reachable from every other state. Also, if k were a toehold domain (not shown), then only complexes A, A3, A33 and A3x would have an outgoing reaction opening that toehold, but the SCC would contain a copy of every complex with an open toehold, connected via the shown three-way and four-way branch migration reactions. Also, if k is a toehold, A3 and A3x would split into two complexes, and the shown SCC would become a transient macrostate. (b) Reject-remote semantics. Only proximal toehold branch migration reactions are allowed, which leads to a highly disconnected state space. Note an extra unnamed intermediate state on the path $\{\mathrm{A}34\to \mathrm{A}4\}$ as we do not use max-helix semantics here.