DNA Computing: 9th International Workshop on DNA Based Computers, DNA9, Madison, WI, USA, June 1-3, 2003. Revised Papers

Hee-Woong Lim, Hae-Man Jang, Sung-Mo Ha, Young-Gyu Chai, Suk-In Yoo, Byoung-Tak Zhang (auth.), Junghuei Chen, John Reif (eds.)3540209301, 9783540209300, 9783540246282

This book constitutes the thoroughly refereed post-proceedings of the 9th International Workshop on DNA Based Computers, DNA9, held in Madison, Wisconsin, USA in June 2003.

The 22 revised full papers presented were carefully selected during two rounds of reviewing and improvement from initially 60 submissions. The papers are organized in topical sections on new experiments and tools, theory, computer simulation and sequence design, self-assembly and autonomous molecular computation, experimental solutions, and new computing models.

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Table of contents :
Front Matter….Pages –
A Lab-on-a-Chip Module for Bead Separation in DNA-Based Concept Learning….Pages 1-9
Parallel Translation of DNA Clusters by VCSEL Array Trapping and Temperature Control with Laser Illumination….Pages 10-18
Chemical Switching and Molecular Logic in Fluorescent-Labeled M-DNA….Pages 19-31
RCA-Based Detection Methods for Resolution Refutation….Pages 32-36
Word Design for Molecular Computing: A Survey….Pages 37-47
Time-Varying Distributed H Systems with Parallel Computations: The Problem Is Solved….Pages 48-54
Deadlock Decidability in Partial Parallel P Systems….Pages 55-60
Languages of DNA Based Code Words….Pages 61-73
Secondary Structure Design of Multi-state DNA Machines Based on Sequential Structure Transitions….Pages 74-85
Analyzing Secondary Structure Transition Paths of DNA/RNA Molecules….Pages 86-90
Self-Assembled Circuit Patterns….Pages 91-107
One Dimensional Boundaries for DNA Tile Self-Assembly….Pages 108-125
Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly….Pages 126-144
A DNA-Based Memory with In Vitro Learning and Associative Recall….Pages 145-156
Efficiency and Reliability of Semantic Retrieval in DNA-Based Memories….Pages 157-169
Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop….Pages 170-179
Mathematical Considerations in the Design of Microreactor-Based DNA Computers….Pages 180-189
Towards a Re-programmable DNA Computer….Pages 190-196
In Vitro Translation-Based Computations….Pages 197-202
Autonomous Biomolecular Computer Modeled after Retroviral Replication….Pages 203-212
Biomolecular Computing by Encoding of Regulated Phosphorylation-Dephosphorylation and Logic of Kinase-Phosphatase in Cells….Pages 213-218
Conformational Addressing Using the Hairpin Structure of Single-Strand DNA….Pages 219-224
Back Matter….Pages –