DNA Computing: 12th International Meeting on DNA Computing, DNA12, Seoul, Korea, June 5-9, 2006, Revised Selected Papers

Mihai Ionescu, Andrei Păun, Gheorghe Păun, Mario J. Pérez-Jiménez (auth.), Chengde Mao, Takashi Yokomori (eds.)9783540490241, 3540490248

This book constitutes the thoroughly refereed post-proceedings of the 11th International Workshop on DNA Based Computers, DNA11, held in London, ON, Canada, in June 2005.

The 34 revised full papers presented were carefully selected during two rounds of reviewing and improvement from an initial total of 79 submissions. The wide-ranging topics include in vitro and in vivo biomolecular computation, algorithmic self-assembly, DNA device design, DNA coding theory, and membrane computing.

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Table of contents :
Front Matter….Pages –
Computing with Spiking Neural P Systems: Traces and Small Universal Systems….Pages 1-16
Minimal Parallelism for Polarizationless P Systems….Pages 17-32
P Systems with Active Membranes Characterize PSPACE….Pages 33-46
All NP-Problems Can Be Solved in Polynomial Time by Accepting Networks of Splicing Processors of Constant Size….Pages 47-57
Length-Separating Test Tube Systems….Pages 58-70
Gene Assembly Algorithms for Ciliates….Pages 71-82
Spectrum of a Pot for DNA Complexes….Pages 83-94
On the Complexity of Graph Self-assembly in Accretive Systems….Pages 95-110
Viral Genome Compression….Pages 111-126
DNA Codes and Their Properties….Pages 127-142
In Search of Optimal Codes for DNA Computing….Pages 143-156
DNA Sequence Design by Dynamic Neighborhood Searches….Pages 157-171
Sequence Design for Stable DNA Tiles….Pages 172-181
Hairpin Structures Defined by DNA Trajectories….Pages 182-194
Design and Simulation of Self-repairing DNA Lattices….Pages 195-214
On Times to Compute Shapes in 2D Tile Self-assembly….Pages 215-222
Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-assembly in Two and Three Dimensions….Pages 223-238
A Mathematical Approach to Cross-Linked Structures in Viral Capsids: Predicting the Architecture of Novel Containers for Drug Delivery….Pages 239-249
A Framework for Modeling DNA Based Molecular Systems….Pages 250-265
Uniquimer: A de Novo DNA Sequence Generation Computer Software for DNA Self-assembly….Pages 266-273
A Probabilistic Model of the DNA Conformational Change….Pages 274-285
Simulations of Microreactors: The Order of Things….Pages 286-297
DNA Hypernetworks for Information Storage and Retrieval….Pages 298-307
Abstraction Layers for Scalable Microfluidic Biocomputers….Pages 308-323
Fuzzy Forecasting with DNA Computing….Pages 324-336
“Reasoning” and “Talking” DNA: Can DNA Understand English?….Pages 337-349
A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes….Pages 350-359
Automating the DNA Computer: Solving n-Variable 3-SAT Problems….Pages 360-373
Local Area Manipulation of DNA Molecules for Photonic DNA Memory….Pages 374-380
Unravel Four Hairpins!….Pages 381-392
Displacement Whiplash PCR: Optimized Architecture and Experimental Validation….Pages 393-403
MethyLogic: Implementation of Boolean Logic Using DNA Methylation….Pages 404-417
Development of DNA Relational Database and Data Manipulation Experiments….Pages 418-427
Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation….Pages 428-438
Back Matter….Pages –