Introduction  

This document proposes a program of Ph.D. dissertation research which will involve experimental investigations of a new technique for DNA-based molecular information processing which I dub cyclic mixture mutagenesis, or CMM for short. CMM was conceived by the supervisor of this research, David Gifford, and has been under intensive conceptual development and analytical study by him, another of his students (1) and myself for roughly the last five months. Our analysis indicates that CMM is computation universal; thus, if it can be made to work as planned, it will serve as the first proof-of-concept demonstrating that general molecular computing is possible, which is an important early step in the development of molecular computation technology. Additionally, CMM is interesting from a biology perspective because we believe that something similar to it could potentially take place in vivo, i.e., in living cells. There is every reason to think that CMM will work, because it was specifically designed from the beginning to be easy to carry out in vitro, i.e., in test tubes in a molecular biology lab.

Although the possible biological ramifications of CMM are interesting, this is to be a Ph.D. proposal in computer science, so let us begin by discussing some of the motivations and background for this research from that discipline's perspective.

Footnotes

 

1.

Julia Khodor, an undergradate in biology and mathematics at MIT.