DNA Computing

1. Front Matter

   Pages I-XI

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2. Self-assembly and Autonomous Molecular Computation

   1. Self-assembling DNA Graphs

      • Phiset Sa-Ardyen, Nataša Jonoska, Nadrian C. Seeman

      Pages 1-9

   2. DNA Nanotubes: Construction and Characterization of Filaments Composed of TX-tile Lattice

      • Dage Liu, John H. Reif, Thomas H. La Bean

      Pages 10-21

   3. The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA

      • John H. Reif

      Pages 22-37

   4. Cascading Whiplash PCR with a Nicking Enzyme

      • Daisuke Matsuda, Masayuki Yamamura

      Pages 38-46

3. Molecular Evolution and Application to Biotechnology

   1. A PNA-mediated Whiplash PCR-based Program for In Vitro Protein Evolution

      • John A. Rose, Mitsunori Takano, Akira Suyama

      Pages 47-60

   2. Engineering Signal Processing in Cells: Towards Molecular Concentration Band Detection

      • Subhayu Basu, David Karig, Ron Weiss

      Pages 61-72

4. Applications to Mathematical Problems

   1. Temperature Gradient-Based DNA Computing for Graph Problems with Weighted Edges

      • Ji Youn Lee, Soo-Yong Shin, Sirk June Augh, Tai Hyun Park, Byoung-Tak Zhang

      Pages 73-84

   2. Shortening the Computational Time of the Fluorescent DNA Computing

      • Yoichi Takenaka, Akihiro Hashimoto

      Pages 85-94

   3. How Efficiently Can Room at the Bottom Be Traded Away for Speed at the Top?

      • Pilar de la Torre

      Pages 95-111

   4. Hierarchical DNA Memory Based on Nested PCR

      • Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba, Azuma Ohuchi

      Pages 112-123

   5. Binary Arithmetic for DNA Computers

      • Rana Barua, Janardan Misra

      Pages 124-132

   6. Implementation of a Random Walk Method for Solving 3-SAT on Circular DNA Molecules

      • Hubert Hug, Rainer Schuler

      Pages 133-142

   7. Version Space Learning with DNA Molecules

      • Hee-Woong Lim, Ji-Eun Yun, Hae-Man Jang, Young-Gyu Chai, Suk-In Yoo, Byoung-Tak Zhang

      Pages 143-155

   8. DNA Implementation of Theorem Proving with Resolution Refutation in Propositional Logic

      • In-Hee Lee, Ji-Yoon Park, Hae-Man Jang, Young-Gyu Chai, Byoung-Tak Zhang

      Pages 156-167

   9. Universal Biochip Readout of Directed Hamiltonian Path Problems

      • David Harlan Wood, Catherine L. Taylor Clelland, Carter Bancroft

      Pages 168-181

5. Nucleic Acid Sequence Design

   1. Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure

      • Mirela Andronescu, Danielle Dees, Laura Slaybaugh, Yinglei Zhao, Anne Condon, Barry Cohen et al.

      Pages 182-195

   2. A PCR-based Protocol for In Vitro Selection of Non-crosshybridizing Oligonucleotides

      • Russell Deaton, Junghuei Chen, Hong Bi, Max Garzon, Harvey Rubin, David Harlan Wood

      Pages 196-204

   3. On Template Method for DNA Sequence Design

      • Satoshi Kobayashi, Tomohiro Kondo, Masanori Arita

      Pages 205-214

   4. From RNA Secondary Structure to Coding Theory: A Combinatorial Approach

      • Christine E. Heitsch, Anne E. Condon, Holger H. Hoos

      Pages 215-228

Biomolecular computing has emerged as an interdisciplinary ?eld that draws - gether chemistry, computer science, mathematics, molecular biology, and physics. Our knowledge on DNA nanotechnology and biomolecular computing increases exponentially with every passing year. The international meeting on DNA Based Computers has been a forum where scientists with di?erent backgrounds, yet sharing a common interest in biomolecular computing, meet and present their latest results. Continuing this tradition, the 8th International Meeting on DNA Based Computers (DNA8) focuses on the current theoretical and experimental results with the greatest impact. Papers and poster presentations were sought in all areas that relate to b- molecular computing, including (but not restricted to): algorithms and appli- tions, analysis of laboratory techniques/theoretical models, computational p- cesses in vitro and in vivo, DNA-computing-based biotechnological applications, DNA devices, error evaluation and correction, in vitro evolution, models of biomolecular computing (using DNA and/or other molecules), molecular - sign, nucleic acid chemistry, and simulation tools. Papers and posters with new experimental results were particularly encouraged. Authors who wished their work to be considered for either oral or poster presentation were asked to select from one of two submission “tracks”: – Track A - Full Paper – Track B - One-Page Abstract For authors with late-breaking results, or who were submitting their manuscript to a scienti?c journal, a one-page abstract, rather than a full paper, could be submitted in Track B. Authors could (optionally) include a preprint of their full paper, for consideration only by the program committee.

• Biocomputing
• Bioinformatics
• DNA Algorithms
• DNA Computers
• DNA computing
• DNA-Based Computing
• Evolutionary Computing
• Molecular Computing
• Resolution
• algorithms
• coding theory
• logic
• optimization
• proving
• theorem proving
• algorithm analysis and problem complexity

• Department of Computer Science, University of Toyko Graduate School of Information Science and Technology, Tokyo, Japan

  Masami Hagiya

• Division of Complex Systems Technology, Hokkaido University Graduate School of Engineering, Sapporo, Japan

  Azuma Ohuchi

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