DNA Computing

1. Front Matter

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2. Self-assembly

   1. Staged Self-assembly: Nanomanufacture of Arbitrary Shapes with O(1) Glues

      • Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Mashhood Ishaque, Eynat Rafalin, Robert T. Schweller et al.

      Pages 1-14

   2. Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications

      • Urmi Majumder, Thomas H. LaBean, John H. Reif

      Pages 15-25

   3. Constant-Size Tileset for Solving an NP-Complete Problem in Nondeterministic Linear Time

      • Yuriy Brun

      Pages 26-35

   4. Solutions to Computational Problems Through Gene Assembly

      • Artiom Alhazov, Ion Petre, Vladimir Rogojin

      Pages 36-45

3. Biomolecular Machines and Automata

   1. Toward Minimum Size Self-Assembled Counters

      • Ashish Goel, Pablo Moisset de Espanés

      Pages 46-53

   2. A Realization of DNA Molecular Machine That Walks Autonomously by Using a Restriction Enzyme

      • Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga, Masayuki Yamamura

      Pages 54-65

   3. Autonomous Programmable Nanorobotic Devices Using DNAzymes

      • John H. Reif, Sudheer Sahu

      Pages 66-78

   4. Multi-fueled Approach to DNA Nano-Robotics

      • Akio Nishikawa, Satsuki Yaegashi, Kazumasa Ohtake, Masami Hagiya

      Pages 79-88

   5. Experimental Validation of the Transcription-Based Diagnostic Automata with Quantitative Control by Programmed Molecules

      • Miki Hirabayashi, Hirotada Ohashi, Tai Kubo

      Pages 89-98

   6. DNA Memory with 16.8M Addresses

      • Masahito Yamamoto, Satoshi Kashiwamura, Azuma Ohuchi

      Pages 99-108

4. Codes for DNA Memories and Computing

   1. Combining Randomness and a High-Capacity DNA Memory

      • Atsushi Kameda, Satoshi Kashiwamura, Masahito Yamamoto, Azuma Ohuchi, Masami Hagiya

      Pages 109-118

   2. Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics

      • Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, Akira Suyama

      Pages 119-129

   3. Dynamic Neighborhood Searches for Thermodynamically Designing DNA Sequence

      • Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

      Pages 130-139

   4. Sequence Design Support System for 4 × 4 DNA Tiles

      • Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Azuma Ohuchi

      Pages 140-145

   5. DNA Codes Based on Stem Similarities Between DNA Sequences

      • Arkadii D’yachkov, Anthony Macula, Vyacheslav Rykov, Vladimir Ufimtsev

      Pages 146-151

5. Novel Techniques for DNA Computing in vitro

   1. Heuristic Solution to a 10-City Asymmetric Traveling Salesman Problem Using Probabilistic DNA Computing

      • David Spetzler, Fusheng Xiong, Wayne D. Frasch

      Pages 152-160

   2. An Approach for Using Modified Nucleotides in Aqueous DNA Computing

      • Angela M. Pagano, Susannah Gal

      Pages 161-169

   3. Modeling Non-specific Binding in Gel-Based DNA Computers

      • Clifford R. Johnson

      Pages 170-181

   4. Stepwise Assembly of DNA Tile on Surfaces

      • Kotaro Somei, Shohei Kaneda, Teruo Fujii, Satoshi Murata

      Pages 182-190

Biomolecular/DNA computing is now well established as an interdisciplinary field where chemistry, computer science, molecular biology, physics, and mathematics come together with the common purpose of fundamental scientific understanding of biology and chemistry and its applications. This international meeting has been the premier forum where scientists with different backgrounds and a common focus meet to present their latest results and entertain visions of the future. In this tradition, about 100 participants converged in Memphis, Tennessee to hold the 13th International Meeting on DNA Computing during June 4–8, 2007, under the auspices of the International Society for Nanoscale Science, Computation and Engineering (ISNSCE) and The University of Memphis. The call for papers encouraged submissions of original, recent, and promising experimental and theoretical results in the field. The Call for Papers elicited some 62 submissions, almost perfectly balanced among the major theoretical and experimental categories. It is evidence of how well the interdisciplinary nature of the conference has truly matured that the major criterion of quality, agreed upon in advance by the Program Committee (PC), produced a nearly balanced program as well across the two major categories, full papers and talks with an abstract only. The program with the greatest perceived impact consisted of 24 papers for plenary oral talks; in addition, 15 full-paper posters and 10 poster abstracts were accepted, of which 5 authors were invited to give five short demos in a new submission category this year. The conference program retained the structure now customary for this meeting.

• DNA algorithms
• DNA coding
• DNA computers
• DNA computing
• algorithms
• automata
• bio-inspired computing
• biocomputing
• bioinformatics
• biomolecular computing
• cellular automata
• complexity theory
• modeling
• robot
• robotics
• algorithm analysis and problem complexity

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