DNA Computing: 13th International Meeting on DNA Computing, DNA13, Memphis, TN, USA, June 4-8, 2007, Revised Selected Papers

Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Mashhood Ishaque, Eynat Rafalin (auth.), Max H. Garzon, Hao Yan (eds.)3540779612, 9783540779612

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.

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Table of contents :
Front Matter….Pages –
Staged Self-assembly: Nanomanufacture of Arbitrary Shapes with O (1) Glues….Pages 1-14
Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications….Pages 15-25
Constant-Size Tileset for Solving an NP-Complete Problem in Nondeterministic Linear Time….Pages 26-35
Solutions to Computational Problems Through Gene Assembly….Pages 36-45
Toward Minimum Size Self-Assembled Counters….Pages 46-53
A Realization of DNA Molecular Machine That Walks Autonomously by Using a Restriction Enzyme….Pages 54-65
Autonomous Programmable Nanorobotic Devices Using DNAzymes….Pages 66-78
Multi-fueled Approach to DNA Nano-Robotics….Pages 79-88
Experimental Validation of the Transcription-Based Diagnostic Automata with Quantitative Control by Programmed Molecules….Pages 89-98
DNA Memory with 16.8M Addresses….Pages 99-108
Combining Randomness and a High-Capacity DNA Memory….Pages 109-118
Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics….Pages 119-129
Dynamic Neighborhood Searches for Thermodynamically Designing DNA Sequence….Pages 130-139
Sequence Design Support System for 4 × 4 DNA Tiles….Pages 140-145
DNA Codes Based on Stem Similarities Between DNA Sequences….Pages 146-151
Heuristic Solution to a 10-City Asymmetric Traveling Salesman Problem Using Probabilistic DNA Computing….Pages 152-160
An Approach for Using Modified Nucleotides in Aqueous DNA Computing….Pages 161-169
Modeling Non-specific Binding in Gel-Based DNA Computers….Pages 170-181
Stepwise Assembly of DNA Tile on Surfaces….Pages 182-190
An Interface for a Computing Model Using Methylation to Allow Precise Population Control by Quantitative Monitoring….Pages 191-200
Hardware Acceleration for Thermodynamic Constrained DNA Code Generation….Pages 201-210
Hardware and Software Architecture for Implementing Membrane Systems: A Case of Study to Transition P Systems….Pages 211-220
Towards a Robust Biocomputing Solution of Intractable Problems….Pages 221-230
Discrete Simulations of Biochemical Dynamics….Pages 231-235
DNA Splicing Systems….Pages 236-245
Asynchronous Spiking Neural P Systems: Decidability and Undecidability….Pages 246-255
On 5′→3′ Sensing Watson-Crick Finite Automata….Pages 256-262
Equivalence in Template-Guided Recombination….Pages 263-272
Watson-Crick Conjugate and Commutative Words….Pages 273-283
DNA Coding Using the Subword Closure Operation….Pages 284-289
Back Matter….Pages –