1. Molecular Computation
Molecular Computing Machineries

2. Sources
Material in this lecture comes from, “Handbook of Natural Computing,” Editors Grzegorz Rosenberg, Thomas Back and Joost N. Kok, Springer 2014.

4. For v not empty, we need to encode the type-(ii) rule in each of the three forms on the left side (alpha, beta, gamma); this is because we need the delta rule for an empty v.

8. Problems:
The input has unexpected structures
Need to use secondary structural property of fully duplex DNAs to discriminate them from partial duplex DNAs (PDDs)

13. And other magic based on Horn programs …
And a whole section on FSMs ….

14. x = the reverse of the complement of v

16. Enzyme based DNA automata

20. B A
And more: strand displacements, DNA tiles, reaction graphs, Whiplash machine ….