This thesis reports an unusual and unexpected journey through intellectual territory entirely new
to me. Who is prepared for such journeys? I was not. Thus my debt is great to those who have
helped me along the way, without whose help I would have been completely lost and uninspired.
There is no way to give sufficient thanks to my advisor, John Hopfield. His encouragement
for me to get my feet wet, and his advice cutting to the bone of each issue, have been invaluable.
John’s policy has been, in his own words, to give his students “enough rope to hang themselves
with.” But he knows full well that a lot of rope is needed to weave macrame. Perhaps the only
possible repayment is in kind: to maintain a high standard of integrity, and when my turn comes,
to provide a nurturing environment for other young minds.
Len Adleman and Ned Seeman have each been mentors during my thesis work. In many ways,
my research can be seen as the direct offspring of their work, combining the notion of using DNA
for computation with the ability to design DNA structures with artificial topology. Both Len and
Ned have provided encouragement, support, and valuable feedback throughout this project.
I would like additionally to thank Ned Seeman and Xiaoping Yang for teaching me how to
do laboratory experiments with DNA. Xiaoping’s patient and careful tutoring provided me with
a solid first step toward becoming a competent experimenter. John Abelson generously made me
welcome to continue my experimenting at Caltech in a friendly and expert environment; I am
deeply grateful to him and to all the members of his laboratory without whose help I could have
done little. For teaching me to use the atomic force microscope, I thank Anca Segall, Bob Moision,
and Ely Rabani; with their encouragement and help I saw the first exciting images of DNA lattices.
Likewise, Rob Rossi’s friendly and spirited management of the Caltech SPM room made doing
science there a breeze.
I am grateful for the encouragement and feedback of my thesis committee: John Abelson,
Yaser Abu-Mostafa, Len Adleman, John Baldeschwieler, Al Barr, and John Hopfield.
Perhaps most influential have been the people in my everyday life. All the members of the
Hopfield group – Carlos Brody, Dawei Dong, Maneesh Sahani, Marcus Mitchell, Sam Roweis,
Sanjoy Majahan, Tom Annau, and Unni Unnikrishnan – have been wonderful to be with, both on
and off duty. Laura Rodriguez has been our guardian angel. Paul Rothemund has been a steady
and stimulating companion throughout this DNA adventure, and it is fair to say that this project
would never have been born without him. Matt Cook has been a source of intellectual inspiration
and joy for many years. I have learned so much from you all. I will miss you all when we are