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Author Chang, Jessica P.

Title Storing clocked programs inside DNA : a simplifying framework for nanocomputing / Jessica P. Chang and Dennis E. Shasha
Published Cham, Switzerland : Springer, ©2011
Online access available from:
Synthesis Digital Library    View Resource Record  


Description 1 online resource (viii, 63 pages) : illustrations (some color)
Series Synthesis lectures on computer science, 1932-1686 ; #3
Synthesis lectures on computer science ; #4. 1932-1228
Contents Acknowledgments -- 1. Introduction -- A short history of DNA computing -- Underlying physical chemistry -- DNA computation and engineering
2. Notation -- State description -- Labeling -- Hybridization -- Nodes -- Transitions -- Spontaneous transitions -- Manual transitions -- Syntactic -- Dynamic behavior -- Stabilization -- Stoichiometry -- User-level state diagram
3. A topological description of DNA computing -- As a cell complex -- State -- Transitions
4. Machines and motifs -- A brief review of DNA construction motifs -- Tape motif -- Walkers and gears -- Polymer growth -- A clocked stored program DNA machine -- Clocked instruction stack -- Linear (straight line) program -- Gating and flow control -- Looping -- Iterated variables -- Considerations -- Example applications -- Future theoretical work
5. Experiment: storing clocked programs in DNA -- Constructing stored instruction stacks -- Introduction -- Overview of methods -- Protocol details -- Experimental conclusions/future directions
6. A clocked DNA programming language -- Existing programming languages may not work -- ParaGAT: a minimalist language for a clocked parallel DNA computer -- Conceptualizing computations in ParaGAT -- An example application in ParaGAT -- Future work
Bibliography -- Authors' biographies -- Index
Summary In the history of modern computation, large mechanical calculators preceded computers. A person would sit there punching keys according to a procedure and a number would eventually appear. Once calculators became fast enough, it became obvious that the critical path was the punching rather than the calculation itself. That is what made the stored program concept vital to further progress. Once the instructions were stored in the machine, the entire computation could run at the speed of the machine. This book shows how to do the same thing for DNA computing. Rather than asking a robot or a person to pour in specific strands at different times in order to cause a DNA computation to occur (by analogy to a person punching numbers and operations into a mechanical calculator), the DNA instructions are stored within the solution and guide the entire computation. We show how to store straight line programs, conditionals, loops, and a rudimentary form of subroutines
Bibliography Includes bibliographical references (pages 57-58) and index
Subject Molecular computers.
Molecular computers -- Programming
Parallel programming (Computer science)
MATHEMATICS -- Infinity.
Molecular computers
Parallel programming (Computer science)
Form Electronic book
Author Shasha, Dennis Elliott.
ISBN 9781608456963