In vitro implementation of finite-state machines
We explore the information processing capabilities and efficiency of DNA computations by giving two different types of implementations of finite-state machines. A ligation-based approach allows input of arbitrary length and can be readily implemented with current biotechnology, but requires sequential input feed and different molecules for different machines. In a second implementation not based on ligation, transitions are represented by reusable molecules, and the input, coded as a molecule, can be introduced at once. We extend the technique for programmable fault-tolerant implementation of nondeterministic finite-state machines by enforcings the basic conditions in the subset constructions that permit efficient computation. All implementations allow optical extraction of the status of the machine.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Garzon, M., Gao, Y., Rose, J., Murphy, R., Deaton, R., Franceschetti, D., & Stevens, S. (1998). In vitro implementation of finite-state machines. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 56-74. https://doi.org/10.1007/bfb0031381