This book constitutes the thoroughly refereed postproceedings of the 10th International Workshop on DNA Based Computers, DNA10, held in Milano, Italy in June 2004.
The 39 revised full papers presented were carefully selected during two rounds of reviewing and improvement from an initial total of 94 submissions. The papers address all current issues in DNA based computing and biomolecular computing ranging from theoretical and methodological issues to implementations and experimental aspects.
Author(s): Artiom Alhazov, Matteo Cavaliere (auth.), Claudio Ferretti, Giancarlo Mauri, Claudio Zandron (eds.)
Series: Lecture Notes in Computer Science 3384 : Theoretical Computer Science and General Issues
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2005
Language: English
Pages: 472
Tags: Computation by Abstract Devices; Algorithm Analysis and Problem Complexity; Artificial Intelligence (incl. Robotics); Bioinformatics; Computer Appl. in Life Sciences
Front Matter....Pages -
Computing by Observing Bio-systems: The Case of Sticker Systems....Pages 1-13
DNA-Based Computation Times....Pages 14-23
Computing Beyond the Turing Limit Using the H Systems....Pages 24-34
Biomolecular Implementation of Computing Devices with Unbounded Memory....Pages 35-49
Characterization of Non-crosshybridizing DNA Oligonucleotides Manufactured In Vitro ....Pages 50-61
Error Free Self-assembly Using Error Prone Tiles....Pages 62-75
On the Computational Complexity of P Automata....Pages 76-89
A Weighted Insertion-Deletion Stacked Pair Thermodynamic Metric for DNA Codes....Pages 90-103
DNA Extraction by XPCR....Pages 104-112
A Method of Error Suppression for Self-assembling DNA Tiles....Pages 113-127
Using Automated Reasoning Systems on Molecular Computing....Pages 128-137
Parallelism in Gene Assembly....Pages 138-148
Splicing Systems for Universal Turing Machines....Pages 149-158
Application of Mismatch Detection Methods in DNA Computing....Pages 159-168
Bond-Free Languages: Formalizations, Maximality and Construction Methods....Pages 169-181
Preventing Undesirable Bonds Between DNA Codewords....Pages 182-191
Testing Structure Freeness of Regular Sets of Biomolecular Sequences....Pages 192-201
Minimum Basin Algorithm: An Effective Analysis Technique for DNA Energy Landscapes....Pages 202-214
Efficient Initial Pool Generation for Weighted Graph Problems Using Parallel Overlap Assembly....Pages 215-223
Partial Words for DNA Coding....Pages 224-234
Accepting Hybrid Networks of Evolutionary Processors....Pages 235-246
Building the Components for a Biomolecular Computer....Pages 247-257
Methods for Manipulating DNA Molecules in a Micrometer Scale Using Optical Techniques....Pages 258-267
From Cells to Computers: Membrane Computing – A Quick Overview....Pages 268-280
The Capacity of DNA for Information Encoding....Pages 281-292
Compact Error-Resilient Computational DNA Tiling Assemblies....Pages 293-307
Toward “Wet” Implementation of Genetic Algorithm for Protein Engineering....Pages 308-318
Programmable Control of Nucleation for Algorithmic Self-assembly....Pages 319-328
DNA Hybridization Catalysts and Catalyst Circuits....Pages 329-343
Complexity of Self-assembled Shapes....Pages 344-354
Aqueous Computing with DNA Hairpin-Based RAM....Pages 355-364
A Programmable Molecular Computer in Microreactors....Pages 365-374
Combinatorial Aspects of Minimal DNA Expressions....Pages 375-388
A Design for Cellular Evolutionary Computation by Using Bacteria....Pages 389-398
An Inexpensive LED-Based Fluorometer Used to Study a Hairpin-Based DNA Nanomachine....Pages 399-409
Designs of Autonomous Unidirectional Walking DNA Devices....Pages 410-425
Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion....Pages 426-444
A Clocked DNA-Based Replicator....Pages 445-457
A Bayesian Algorithm for In Vitro Molecular Evolution of Pattern Classifiers....Pages 458-467
Back Matter....Pages -
