Erik's Molecular Computation page: Resources

Some references and resources for molecular computation.

Many good resources can be found via home pages of the people above. Laura Landweber recommends the CMS Molecular Biology Resources. There's also a page maintained by Ian Brandt, another by Yali Friedman. Chris Love and James Ellenbogen have some comments from the perspective of nanotechnology. For general molecular biology information, I've found the following sites useful: Paul Hengen, Pedro's BioMolecular Research Tools, Fabricio dos Santos. Anderson's TCG is a great resources for commercial information (although now it requires registration).

I am beginning to collect a list of computer programs that may be helpful estimating physical properties of DNA and other such things. I am also collecting useful on-line references for DNA chemistry and available products (some of which are commercial company web pages, of course).


Where to start.

Learning the essentials of molecular biology. As for textbooks, "DNA Replication" by Kornberg & Baker gives a good introduction to numerous enzymes that operate on DNA, while "Molecular Biology of the Cell" by Alberts ... Watson is an excellent introduction to the whole field. The golden recipe book of molecular biology techniques is "Molecular Cloning: A Laboratory Manual" by Sambrook, Fritsch, and Maniatis. Even if you never plan to get into the lab yourself, this will give you a sense of what's involved in experiments, what's easy and what's hard, and all the clever tricks that people already use in day-to-day existence. Also essential to making DNA computing work in the laboratory is a good understanding of quantitative biochemistry, where possible. There is more to PCR, for example, than what the cartoons make it out to be.

Learning the essentials of DNA computation. As for introduction to the ideas of molecular computation, after Len Adleman's original paper in Science, I'd recommend either "Breaking DES Using a Molecular Computer" by Dan Boneh, Richard Lipton and Chris Dunworth, or "On the Computational Power of DNA" by Dan Boneh, Richard Lipton, Chris Dunworth and Jiri Sgall. These papers present a good basic model against which new models can be compared. For example, people suggesting how addition and multiplication can be done in DNA should realize that Boneh's circuit model already quite elegantly encompasses both these operations, and is fully parallel. On a historical note, a wonderful, if fanciful, description of an enzymatic Turing Machine (inspired by RNA polymerase) is given in Charles Bennett's "The Thermodynamics of Computation -- A Review" (International Journal of Theoretical Physics, v 21, n 12, 1982).

Learning the essentials of computer science. Two of my favorite texts are "Computation: Finite and Infinite Machines" by Marvin Minsky, and "Computational Complexity" by Christos Papadimitriou.


The proceedings from the 1st, 2nd, and 3rd DNA Based Computes workshops are being published. Currently, the 1st volume is available from the AMS DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume Twenty Seven: "DNA Based Computers - Proceedings of a DIMACS Workshop, April 4, 1995", Editors: Richard J. Lipton and Eric B. Baum

These books may be obtained from the AMS. To order through AMS contact the AMS Customer Services Department, P.O. Box 6248, Providence, Rhode Island 02940-6248 USA. For Visa, Mastercard, Discover, and American Express orders call 1-800-321-4AMS.


Len Adleman maintains a (seldom-used) mailing list for molecular computation: dna@pollux.usc.edu . Join it via dna-request@pollux.usc.edu. A new mailing list (intended, I believe, for sharing lab techniques and knowledge) is being organized by Julia Khodor. bio-comp@mit.edu is the address. If you want to be on this new mailing list, please send a message to (jkhodor@mit.edu) with the subject "subscribe", and the message body

"subscribe "


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winfree@hope.caltech.edu