Acknowledgments

First, of course, I owe a great deal to David Gifford, who conceived the DNA computation project, invited me to work on it, and has been the major force guiding its evolution. Secondly, Julia Khodor has been a most excellent research partner, a pleasure to work with; she has made many invaluable contributions to the project, including efficient work in both the laboratory and the library, and the designs for several DNA computers.

Additionally, the research to date has benefited a great deal from discussions with many interested individuals. Leonard Lerman from the MIT Biology department pointed us towards the DNA biochemistry information we needed. K. Makarova and Victor Solovyev from Russia kindly provided us with their program for analyzing oligonucleotide primers. Mark Torrance helped me work out how to do gradual transformation of machine states. Tim Boykett pointed me towards Bennett's work on logical reversibility. Carl Witty helped me work out the relationship between irreversibility and forward progress. Marvin Minsky confirmed that his universal Turing machine was the smallest known. Tom Knight read and commented on an earlier version of some of the material in this document. And Jody Alperin originally inspired my foray into biology, and has been an everlasting source of encouragement and moral support throughout.

Finally, this research could not have taken place without the generous help of Douglas Melton of Harvard University and the members of his laboratory, who have kindly provided facilities and assistance for the experimental work which is the most vital part of the project. Doug himself has also provided valuable feedback concerning possibilities for biological applications of this work. All of us on the project thank him and his lab members warmly for their continuing contributions.

This material is based upon work supported under a National Science Foundation Graduate Fellowship. Any opinions, findings, conclusions or recommendations expressed in this publication are those of the author and do not necessarily reflect the views of the National Science Foundation.