DNA Computing and Molecular Programming

1. Front Matter

   PDF

2. Invited Talks

   1. Cooperative Assembly Systems

      • Vincent Danos, Heinz Koeppl, John Wilson-Kanamori

      Pages 1-20

   2. The Computer Science of Molecular Programming

      • Jack H. Lutz

      Pages 21-21

   3. An Autonomous DNA Nanodevice Captures pH Maps of Living Cells in Culture and in Vivo

      • Sunaina Surana, Souvik Modi, Yamuna Krishnan

      Pages 22-31

   4. Cooperation in an All-RNA Network

      • Nilesh Vaidya, Jessica Mellor, Niles Lehman

      Pages 32-32

   5. Designer DNA Architectures for Bionanotechnology

      • Hao Yan

      Pages 33-33

3. Contributed Papers

   1. An Improved DNA-Sticker Addition Algorithm and Its Application to Logarithmic Arithmetic

      • Mark G. Arnold

      Pages 34-48

   2. Graph-Theoretic Formalization of Hybridization in DNA Sticker Complexes

      • Robert Brijder, Joris J. M. Gillis, Jan Van den Bussche

      Pages 49-63

   3. Localized Hybridization Circuits

      • Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

      Pages 64-83

   4. Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems

      • Anne Condon, Alan Hu, Ján Maňuch, Chris Thachuk

      Pages 84-99

   5. One-Dimensional Staged Self-assembly

      • Erik D. Demaine, Sarah Eisenstat, Mashhood Ishaque, Andrew Winslow

      Pages 100-114

   6. Computing Maximal Kleene Closures That Are Embeddable in a Given Constrained DNA Language

      • Stavros Konstantinidis, Nicolae Santean

      Pages 115-129

   7. Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems

      • Matthew R. Lakin, Andrew Phillips

      Pages 130-144

   8. Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-assembly

      • Tuomo Lempiäinen, Eugen Czeizler, Pekka Orponen

      Pages 145-159

   9. Multivalent Random Walkers — A Model for Deoxyribozyme Walkers

      • Mark J. Olah, Darko Stefanovic

      Pages 160-174

   10. Exact Shapes and Turing Universality at Temperature 1 with a Single Negative Glue

       • Matthew J. Patitz, Robert T. Schweller, Scott M. Summers

       Pages 175-189

   11. Autonomous Resolution Based on DNA Strand Displacement

       • Alfonso Rodríguez-Patón, Iñaki Sainz de Murieta, Petr Sosík

       Pages 190-203

   12. Multiple Molecular Spiders with a Single Localized Source—The One-Dimensional Case

       • Oleg Semenov, Mark J. Olah, Darko Stefanovic

       Pages 204-216

4. Back Matter

   PDF

This book constitutes the refereed proceedings of the 17th International Conference on DNA Computing and Molecular Programming, DNA17, held in Pasadena, CA, USA, in September 2011.
The 12 revised full papers presented together with 5 invited talks were carefully selected from numerous submissions. Research in DNA computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. This annual meeting is the premier forum where scientists with diverse backgrounds come together with the common purpose of advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.

• DNA computing
• DNA encodings
• algorithm
• complexity
• regular language
• algorithm analysis and problem complexity
• data structures

• Microsoft Research, Cambridge, UK

  Luca Cardelli

• Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Boston, USA

  William Shih

Policies and ethics