String tile models for DNA computing by self-assembly

  • Erik Winfree
  • Tony Eng
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2054)

Abstract

This paper investigates computation by linear assemblies of complex DNA tiles, which we call string tiles. By keeping track of the strands as they weave back and forth through the assembly, we show that surprisingly sophisticated calculations can be performed using linear self-assembly. Examples range from generating an addition table to providing O(1) solutions to CNF-SAT and DHPP. We classify the families of languages that can be generated by various types of DNA molecules, and establish a correspondence to the existing classes ET0Lml and ET0Lfin. Thus, linear self-assembly of string tiles can generate the output lan- guages of finite-visit Turing Machines.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Erik Winfree
    • 1
  • Tony Eng
    • 2
  • Grzegorz Rozenberg
    • 3
    • 4
  1. 1.Department of Computer ScienceUniversity of Colorado at BoulderBoulderUSA
  2. 2.Depts. of Computer Science and CNSCalifornia Institute of TechnologyPasadenaUSA
  3. 3.Laboratory for Computer ScienceMassachusetts Institute of TechnologyCambridgeUSA
  4. 4.Institute of Advanced Computer Science (LIACS)Leiden UniversityLeidenThe Netherlands

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