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DNA Based Computers V
Edited by: Erik Winfree, California Institute of Technology, Pasadena, CA, and David K. Gifford, Massachusetts Institute of Technology, Cambridge, MA
A co-publication of the AMS and DIMACS.
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DIMACS: Series in Discrete Mathematics and Theoretical Computer Science
2000; 249 pp; hardcover
Volume: 54
ISBN-10: 0-8218-2053-2
ISBN-13: 978-0-8218-2053-7
List Price: US$80
Member Price: US$64
Order Code: DIMACS/54
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This proceedings volume presents the talks from the Fifth Annual Meeting on DNA Based Computers held at MIT. The conference brought together researchers and theorists from many disciplines who shared research results in biomolecular computation.

Two styles of DNA computing were explored at the conference: 1) DNA computing based on combinatorial search, where randomly created DNA strands are used to encode potential solutions to a problem, and constraints induced by the problem are used to identify DNA strands that are solution witnesses; and 2) DNA computing based on finite-state machines, where the state of a computation is encoded in DNA, which controls the biochemical steps that advance the DNA-based machine from state to state.

Featured articles include discussions on the formula satisfiability problem, self-assembly and nanomachines, simulation and design of molecular systems, and new theoretical approaches.

Co-published with the Center for Discrete Mathematics and Theoretical Computer Science beginning with Volume 8. Volumes 1-7 were co-published with the Association for Computer Machinery (ACM).

Readership

Graduate students and research mathematicians interested in computer science; computer scientists; molecular biologists, biochemists, and physicists interested in how molecular systems compute.

Reviews

"Overall this volume offers very enjoyable reading for someone who is interested in this topic ... As the editors conclude ... the future of the field looks bright."

-- SIGACT News

Table of Contents

  • D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber -- When the Knight falls: On constructing an RNA computer
  • H. Yoshida and A. Suyama -- Solution to 3-SAT by breadth first search
  • D. H. Wood, J. Chen, E. Antipov, B. Lemieux, and W. Cedeño -- In vitro selection for a OneMax DNA evolutionary computation
  • B. Bloom and C. Bancroft -- Liposome mediated biomolecular computation
  • K. Chen and E. Winfree -- Error correction in DNA computing: Misclassification and strand loss
  • A. P. Mills, Jr., B. Yurke, and P. M. Platzman -- DNA analog vector algebra and physical constraints on large-scale DNA-based neural network computation
  • A. Marathe, A. E. Condon, and R. M. Corn -- On combinatorial DNA word design
  • M. Garzon, R. J. Deaton, and J. A. Rose -- Soft molecular computing
  • M. Yamamoto, J. Yamashita, T. Shiba, T. Hirayama, S. Takiya, K. Suzuki, M. Munekata, and A. Ohuchi -- A study on the hybridization process in DNA computing
  • A. J. Hartemink, T. S. Mikkelsen, and D. K. Gifford -- Simulating biological reactions: A modular approach
  • T. H. LaBean, E. Winfree, and J. H. Reif -- Experimental progress in computation by self-assembly of DNA tilings
  • M. G. Lagoudakis and T. H. LaBean -- 2D DNA self-assembly for satisfiability
  • T. Yokomori -- YAC: Yet another computation model of self-assembly
  • A. J. Turberfield, B. Yurke, and A. P. Mills, Jr. -- DNA hybridization catalysts and molecular tweezers
  • M. P. Robertson, J. Hesselberth, J. C. Cox, and A. D. Ellington -- Designing and selecting components for nucleic acid computers
  • A. Ehrenfeucht, H. J. Hoogeboom, G. Rozenberg, and N. van Vugt -- Forbidding and enforcing
  • L. Kari and L. F. Landweber -- Computational power of gene rearrangement
  • G. Păun and T. Yokomori -- Membrane computing based on splicing
  • A. Gehani, T. H. LaBean, and J. H. Reif -- DNA-based cryptography
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