Open Questions: DNA and Molecular Computing

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See also: Combinatorics, graph theory, and computation -- Quantum information and computing

Introduction

Optical computing

DNA computing

Molecular computing


Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction



Recommended references: Web sites

Site indexes

Galaxy: DNA-Based Computing
Categorized site directory. Entries usually include descriptive annotations.
DNA Computers
Links to articles in the popular media, some research papers, and home pages of people involved with DNA computers, by Ian Brandt.


Sites with general resources

Erik's Molecular Computation Page
By Eric Winfree. Contains information, publications, references, and external links.
Massively Parallel Computation by DNA
Brief page by Mitsunori Ogihara on his researach, with list of publications.
Caltech Initiative in Computational Molecular Biology
About the research program at Caltech on "the interface between the Biological and the Physical / Chemical / Computational sciences."
Len Adelman
Home page of a major contributor to the subject of DNA computing. Adelman is the principle investigator at the Laboratory for Molecular Science. The site contains references to relevant lectures and papers.
Laboratory for Molecular Science
Work at the laboratory includes DNA computing and self assembly. There is a useful short list of frequently asked questions, containing some external links.
A Bibliography of Molecular Computation and Splicing Systems
Very extensive list, with links to materials that are online.


Surveys, overviews, tutorials

DNA computing
Article from Wikipedia.
How DNA Computers Will Work
Breezy overview for a general audience at the How Stuff Works site.
Turning DNA into Logic Gates
September 2000 Scientific American news article about one way to make a DNA computer.
DNA-Based Computers Could Race Past Supercomputers, Researchers Predict
November 28, 1997 article on DNA computation.
DNA Computing and Informatics at Surfaces
A paper by Robert M. Corn, Lloyd M. Smith, and Anne E. Condon on "the development and characterization of complex mixtures of DNA molecules attached to surfaces."
The ABC of DNA Computing
Article by Tony Phillips with a mathematical flavor. Provides a very good overview of DNA computing by consideration of the directed hamiltonian path problem, which is known to be "NP-complete".


Recommended references: Magazine/journal articles

Smart DNA: Programming the Molecule of Life for Work and Play
Joanne Macdonald; Darko Stefanovic; Milan N. Stojanovic
Scientific American, November 2008
Bringing DNA Computers to Life
Ehud Shapiro; Yaakov Benenson
Scientific American, April 2006
Moletronics Will Change Everything
Rick Overton
Wired, July 2000, pp. 240-251.
Moletronics -- the implementation of computational algorithms by chemical processes -- may be a successor to semiconductor technology. A variety of approaches are being explored, but breakthroughs will be required before silicon technology reaches its limits around 2015.
Computing with Molecules
Mark A. Reed; James M. Tour
Scientific American, June 2000, pp. 86-93
Molecules that act as switches, wires, and memory elements have been produced in the laboratory. But a great deal more research will be required to use these elements for practical computation.
Molecular Computing
David Rotman
Technology Review, May-June 2000, pp. 52-58
Individual organic molecules only a few nanometers in size may be able to function as switches in elecronic logic and memory devices.
Biological Computing
Simson L. Garfinkel
Technology Review, May-June 2000, pp. 70-77
The ability of genes to be switched "on" and "off" may be more than just a metaphor. The switching of genes by other genes through the proteins they code for is real and could potentially be harnessed to allow "programming" of living cells.
DNA Computing
Antonio Regalado
Technology Review, May-June 2000, pp. 80-84
Algorithms as used in present computers and not the only model for "computation". The ability of single strands of DNA to pair off very precisely with specific other strands may be usable to "program" the construction of nanoscale objects and materials.
Physics and the Information Revolution
Joel Birnbaum; R. Stanley Williams
Physics Today, January 2000, pp. 38-42
Physical and economic limits on the speed and density of silicon-based computing technology are gradually being approached. Various possible follow-on technologies exist, but major breakthroughs will be required.
Computing After Silicon
David Rotman
Technology Review, September/October 1999, pp. 92-96
Interview with Stan Williams of Hewlett-Packard's research lab on the question of what can replace silicon technology, which may reach its limits in only 10 years.
A Continuous Model of Computation
Joseph F. Traub
Physics Today, May 1999, pp. 39-43
The Turing-machine model of computation has been dominant for the last 50 years. Other models may be better suited to non-electronic technologies and many of the types of problems that concern physicists.
Computing with DNA
Leonard M. Adelman
Scientific American, August 1998, pp. 54-61
Short pieces of DNA in a test tube can solve computational problems by combining, growing, and recombining. Successful experiments with this technique are redefining how we think of "computation".
DNA Computing: Arrival of Biological Mathematics
Lila Kari
Mathematical Intelligencer, Spring 1997, pp. 9-22
The author explains the basics of DNA computing and give examples. She then looks at more theoretical aspects and raises the question of how different this model of computing is from the traditional idea.
Protein-Based Computers
Roger R. Birge
Scientific American, March 1995, pp. 90-95
Biological molecules may enable fabrication of faster and more compact data storage devices. Possible computer applications include three-dimensional memories, neural networks, and more parallel processing.


Recommended references: Books


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