DNA Computing and Molecular Programming

1. Front Matter

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2. Filter Position in Networks of Evolutionary Processors Does Not Matter: A Direct Proof

   • Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Jose M. Sempere

   Pages 1-11

3. Strand Algebras for DNA Computing

   • Luca Cardelli

   Pages 12-24

4. A Domain-Specific Language for Programming in the Tile Assembly Model

   • David Doty, Matthew J. Patitz

   Pages 25-34

5. Limitations of Self-assembly at Temperature One

   • David Doty, Matthew J. Patitz, Scott M. Summers

   Pages 35-44

6. Advancing the Deoxyribozyme-Based Logic Gate Design Process

   • M. Leigh Fanning, Joanne Macdonald, Darko Stefanovic

   Pages 45-54

7. DNA Chips for Species Identification and Biological Phylogenies

   • Max H. Garzon, Tit-Yee Wong, Vinhthuy Phan

   Pages 55-66

8. Renewable, Time-Responsive DNA Logic Gates for Scalable Digital Circuits

   • Ashish Goel, Morteza Ibrahimi

   Pages 67-77

9. Self-assembly of the Discrete Sierpinski Carpet and Related Fractals

   • Steven M. Kautz, James I. Lathrop

   Pages 78-87

10. Automatic Design of DNA Logic Gates Based on Kinetic Simulation

    • Ibuki Kawamata, Fumiaki Tanaka, Masami Hagiya

    Pages 88-96

11. Design of a Biomolecular Device That Executes Process Algebra

    • Urmi Majumder, John H. Reif

    Pages 97-105

12. NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots

    • Ján Maňuch, Chris Thachuk, Ladislav Stacho, Anne Condon

    Pages 106-115

13. The Effect of Malformed Tiles on Tile Assemblies within kTAM

    • Ya Meng, Navin Kashyap

    Pages 116-125

14. Positional State Representation and Its Transition Control for Photonic DNA Automaton

    • Hiroto Sakai, Yusuke Ogura, Jun Tanida

    Pages 126-136

15. Construction of AND Gate for RTRACS with the Capacity of Extension to NAND Gate

    • Yoko Sakai, Yoriko Mawatari, Kiyonari Yamasaki, Koh-ichiroh Shohda, Akira Suyama

    Pages 137-143

16. Time-Complexity of Multilayered DNA Strand Displacement Circuits

    • Georg Seelig, David Soloveichik

    Pages 144-153

17. Distributed Agreement in Tile Self-assembly

    • Aaron Sterling

    Pages 154-163

18. Back Matter

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This book constitutes the thoroughly refereed post-conference proceedings of the 15th International Meeting on DNA Computing, DNA15, held in Fayetteville, AR, USA, in June 2009. The 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 38 submissions. The papers feature current interdisciplinary research in molecular-scale manipulation of matter - in particular, implementation of nanoscale computation and programmed assembly of materials are of interest, thus reflecting a broader scope beyond DNA-based nanotechnology and computation.

• DNA
• DNA computers
• DNA computing
• DNA devices
• DNA-based computing
• algorithms
• automata
• bio-inspired computing
• biocomputing
• bioinformatics
• biomolecular computing
• cellular automata
• gene assembly
• logic g
• nanotechnology
• algorithm analysis and problem complexity

• Dept. of Computer Science and Computer Engineering, JBHT - CSCE 504, 1 University of Arkansas, Fayetteville, USA

  Russell Deaton

• Department of Life Science and Institute of Physics Graduate school of Arts and Sciences, The University of Tokyo, Tokyo, Japan

  Akira Suyama

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