DNA Computing and Molecular Programming

1. Front Matter

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2. Improving Efficiency of 3-SAT-Solving Tile Systems

   • Yuriy Brun

   Pages 1-12

3. Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems

   • Ho-Lin Chen, Ming-Yang Kao

   Pages 13-24

4. Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement

   • Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki

   Pages 25-36

5. Negative Interactions in Irreversible Self-assembly

   • David Doty, Lila Kari, Benoît Masson

   Pages 37-48

6. Search and Validation of Short Genome-Wide Biomarkers for Bacterial Biological Phylogenies

   • Max H. Garzon, Tit-Yee Wong

   Pages 49-58

7. High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices

   • Nikhil Gopalkrishnan, Harish Chandran, John Reif

   Pages 59-70

8. Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly

   • Mika Göös, Pekka Orponen

   Pages 71-82

9. Operation of a DNA-Based Autocatalytic Network in Serum

   • Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes

   Pages 83-88

10. Triangular Tile Self-assembly Systems

    • Lila Kari, Shinnosuke Seki, Zhi Xu

    Pages 89-99

11. Randomized Self Assembly of Rectangular Nano Structures

    • Vamsi Kundeti, Sanguthevar Rajasekaran

    Pages 100-111

12. Design of a Functional Nanomaterial with Recognition Ability for Constructing Light-Driven Nanodevices

    • Xingguo Liang, Toshio Mochizuki, Taiga Fujii, Hiromu Kashida, Hiroyuki Asanuma

    Pages 112-122

13. Efficient Turing-Universal Computation with DNA Polymers

    • Lulu Qian, David Soloveichik, Erik Winfree

    Pages 123-140

14. Reversible Transition of Photonic DNA Automaton Using Hairpin-DNA Responding to a Single Kind of Photonic Signal

    • Hiroto Sakai, Yusuke Ogura, Jun Tanida

    Pages 141-146

15. Simple Evolution of Complex Crystal Species

    • Rebecca Schulman, Erik Winfree

    Pages 147-161

16. Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions

    • David Yu Zhang

    Pages 162-175

17. DNA-Based Fixed Gain Amplifiers and Linear Classifier Circuits

    • David Yu Zhang, Georg Seelig

    Pages 176-186

18. Back Matter

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This book constitutes the thoroughly refereed post-conference proceedings of the 16th International Conference on DNA Computing and Molecular Programming, DNA16, held in Hong Kong, China, in June 2010. The 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 59 submissions. The papers are well balanced between theoretical and experimental work and address all areas that relate to biomolecular computing, including demonstrations of biomolecular computing, theoretical models of biomolecular computing, biomolecular algorithms, computational processes in vitro and in vivo, analysis and theoretical models of laboratory techniques, biotechnological and other applications of DNA computing, DNA nanostructures, DNA devices such as DNA motors, DNA error evaluation and correction, in vitro evolution, molecular design, self-assembled systems, nucleic acid chemistry, and simulation tools.

• DNA circuit
• DNA computing
• DNA devices
• DNA hybridization
• DNA logic gate
• DNA nanostructure
• DNA-based computing
• algorithms
• automata
• biocomputing
• bioinformatics
• biomolecular computing
• cellular automata
• complexity
• logic gate
• molecular computer
• molecular computing
• molecular programming
• nanotechnology
• negative bond strength
• algorithm analysis and problem complexity

• Department of Biosciences and Informatics, Keio University, Yokohama, Japan

  Yasubumi Sakakibara

• Department of Chemical Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China

  Yongli Mi

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