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.
Author(s): Yuliy Baryshnikov, Ed Coffman, Nadrian Seeman, Teddy Yimwadsana (auth.), Alessandra Carbone, Niles A. Pierce (eds.)
Series: Lecture Notes in Computer Science 3892 : Theoretical Computer Science and General Issues
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2006
Language: English
Pages: 444
Tags: Computation by Abstract Devices; Algorithm Analysis and Problem Complexity; Artificial Intelligence (incl. Robotics); Bioinformatics; Computer Appl. in Life Sciences
Front Matter....Pages -
Self-correcting Self-assembly: Growth Models and the Hammersley Process....Pages 1-11
Recognizing DNA Splicing....Pages 12-26
On Computational Properties of Template-Guided DNA Recombination....Pages 27-37
Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks....Pages 38-54
DNA Recombination by XPCR....Pages 55-66
An Algorithm for SAT Without an Extraction Phase....Pages 67-80
Sensitivity and Capacity of Microarray Encodings....Pages 81-95
Simple Operations for Gene Assembly....Pages 96-111
Counting Time in Computing with Cells....Pages 112-128
On Bounded Symport/Antiport P Systems....Pages 129-143
Expectation and Variance of Self-assembled Graph Structures....Pages 144-157
Hairpin Structures in DNA Words....Pages 158-170
Efficient Algorithm for Testing Structure Freeness of Finite Set of Biomolecular Sequences....Pages 171-180
Communicating Distributed H Systems: Optimal Results with Efficient Ways of Communication....Pages 181-192
Intensive In Vitro Experiments of Implementing and Executing Finite Automata in Test Tube....Pages 193-202
Development of an In Vivo Computer Based on Escherichia coli ....Pages 203-212
Control of DNA Molecules on a Microscopic Bead Using Optical Techniques for Photonic DNA Memory....Pages 213-223
Linearizer and Doubler : Two Mappings to Unify Molecular Computing Models Based on DNA Complementarity....Pages 224-235
Analysis and Simulation of Dynamics in Probabilistic P Systems....Pages 236-247
Experimental Validation of DNA Sequences for DNA Computing: Use of a SYBR Green I Assay....Pages 248-256
Complexity of Graph Self-assembly in Accretive Systems and Self-destructible Systems....Pages 257-274
Designing Nucleotide Sequences for Computation: A Survey of Constraints....Pages 275-289
A Self-assembly Model of Time-Dependent Glue Strength....Pages 290-304
Complexity of Compact Proofreading for Self-assembled Patterns....Pages 305-324
A Microfluidic Device for DNA Tile Self-assembly....Pages 325-335
Photo- and Thermoregulation of DNA Nanomachines....Pages 336-346
Chain Reaction Systems Based on Loop Dissociation of DNA....Pages 347-358
A Local Search Based Barrier Height Estimation Algorithm for DNA Molecular Transitions....Pages 359-370
Specificity of Hybridization Between DNA Sequences Based on Free Energy....Pages 371-379
A Poor Man’s Microfluidic DNA Computer....Pages 380-386
Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences....Pages 387-398
Design of Autonomous DNA Cellular Automata....Pages 399-416
Use of DNA Nanodevices in Modulating the Mechanical Properties of Polyacrylamide Gels....Pages 417-426
Molecular Learning of wDNF Formulae....Pages 427-437
Back Matter....Pages -
