Ebook: DNA Computing: 7th International Workshop on DNA-Based Computers, DNA7 Tampa, FL, USA, June 10–13, 2001 Revised Papers

This book constitutes the thoroughly refereed post-proceedings of the 7th International Workshop on DNA-Based Computers, DNA7, held in Tampa, Florida, USA, in June 2001.
The 26 revised full papers presented together with 9 poster papers were carefully reviewed and selected from 44 submissions. The papers are organized in topical sections on experimental tools, theoretical tools, probabilistic computational models, computer simulation and sequence design, algorithms, experimental solutions, nano-tech devices, biomimetic tools, new computing models, and splicing systems and membranes.

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This book constitutes the thoroughly refereed post-proceedings of the 7th International Workshop on DNA-Based Computers, DNA7, held in Tampa, Florida, USA, in June 2001.
The 26 revised full papers presented together with 9 poster papers were carefully reviewed and selected from 44 submissions. The papers are organized in topical sections on experimental tools, theoretical tools, probabilistic computational models, computer simulation and sequence design, algorithms, experimental solutions, nano-tech devices, biomimetic tools, new computing models, and splicing systems and membranes.
Content:
Front Matter....Pages I-XI
An Object Oriented Simulation of Real Occurring Molecular Biological Processes for DNA Computing and Its Experimental Verification....Pages 1-13
Towards Optimization of PCR Protocol in DNA Computing....Pages 14-22
DNASequenceGenerator: A Program for the Construction of DNA Sequences....Pages 23-32
DNA Computing in Microreactors....Pages 33-45
Cascadable Hybridisation Transfer of Specific DNA between Microreactor Selection Modules....Pages 46-56
Coding Properties of DNA Languages....Pages 57-69
Boundary Components of Thickened Graphs....Pages 70-81
Population Computation and Majority Inference in Test Tube....Pages 82-91
DNA Starts to Learn Poker....Pages 92-103
PNA-mediated Whiplash PCR....Pages 104-116
Biomolecular Computation in Virtual Test Tubes....Pages 117-128
Developing Support System for Sequence Design in DNA Computing....Pages 129-137
The Fidelity of the Tag-Antitag System....Pages 138-149
PUNCH: An Evolutionary Algorithm for Optimizing Bit Set Selection....Pages 150-160
Solving Knapsack Problems in a Sticker Based Model....Pages 161-171
A Clause String DNA Algorithm for SAT....Pages 172-181
A Proposal of DNA Computing on Beads with Application to SAT Problems....Pages 182-190
Aqueous Solutions of Algorithmic Problems: Emphasizing Knights on a 3 ? 3....Pages 191-202
Solutions of Shortest Path Problems by Concentration Control....Pages 203-212
Another Realization of Aqueous Computing with Peptide Nucleic Acid....Pages 213-222
Experimental Confirmation of the Basic Principles of Length-only Discrimination....Pages 223-230
Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability....Pages 231-247
Operation of a Purified DNA Nanoactuator....Pages 248-257
DNA Scissors....Pages 258-268
A Realization of Information Gate by Using Enterococcus faecalis Pheromone System....Pages 269-278
Patterns of Micronuclear Genes in Ciliates....Pages 279-289
Peptide Computing - Universality and Complexity....Pages 290-299
Programmed Mutagenesis Is a Universal Model of Computation....Pages 300-307
Horn Clause Computation by Self-assembly of DNA Molecules....Pages 308-320
DNA-based Parallel Computation of Simple Arithmetic....Pages 321-328
On P Systems with Global Rules....Pages 329-339
Computing with Membranes: Variants with an Enhanced Membrane Handling....Pages 340-349
Towards an Electronic Implementation of Membrane Computing: A Formal Description of Non-deterministic Evolution in Transition P Systems....Pages 350-359
Insertion-Deletion P Systems....Pages 360-370
A Universal Time-Varying Distributed H System of Degree 1....Pages 371-380
A Note on Graph Splicing Languages....Pages 381-390
Back Matter....Pages 391-392

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This book constitutes the thoroughly refereed post-proceedings of the 7th International Workshop on DNA-Based Computers, DNA7, held in Tampa, Florida, USA, in June 2001.
The 26 revised full papers presented together with 9 poster papers were carefully reviewed and selected from 44 submissions. The papers are organized in topical sections on experimental tools, theoretical tools, probabilistic computational models, computer simulation and sequence design, algorithms, experimental solutions, nano-tech devices, biomimetic tools, new computing models, and splicing systems and membranes.
Content:
Front Matter....Pages I-XI
An Object Oriented Simulation of Real Occurring Molecular Biological Processes for DNA Computing and Its Experimental Verification....Pages 1-13
Towards Optimization of PCR Protocol in DNA Computing....Pages 14-22
DNASequenceGenerator: A Program for the Construction of DNA Sequences....Pages 23-32
DNA Computing in Microreactors....Pages 33-45
Cascadable Hybridisation Transfer of Specific DNA between Microreactor Selection Modules....Pages 46-56
Coding Properties of DNA Languages....Pages 57-69
Boundary Components of Thickened Graphs....Pages 70-81
Population Computation and Majority Inference in Test Tube....Pages 82-91
DNA Starts to Learn Poker....Pages 92-103
PNA-mediated Whiplash PCR....Pages 104-116
Biomolecular Computation in Virtual Test Tubes....Pages 117-128
Developing Support System for Sequence Design in DNA Computing....Pages 129-137
The Fidelity of the Tag-Antitag System....Pages 138-149
PUNCH: An Evolutionary Algorithm for Optimizing Bit Set Selection....Pages 150-160
Solving Knapsack Problems in a Sticker Based Model....Pages 161-171
A Clause String DNA Algorithm for SAT....Pages 172-181
A Proposal of DNA Computing on Beads with Application to SAT Problems....Pages 182-190
Aqueous Solutions of Algorithmic Problems: Emphasizing Knights on a 3 ? 3....Pages 191-202
Solutions of Shortest Path Problems by Concentration Control....Pages 203-212
Another Realization of Aqueous Computing with Peptide Nucleic Acid....Pages 213-222
Experimental Confirmation of the Basic Principles of Length-only Discrimination....Pages 223-230
Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability....Pages 231-247
Operation of a Purified DNA Nanoactuator....Pages 248-257
DNA Scissors....Pages 258-268
A Realization of Information Gate by Using Enterococcus faecalis Pheromone System....Pages 269-278
Patterns of Micronuclear Genes in Ciliates....Pages 279-289
Peptide Computing - Universality and Complexity....Pages 290-299
Programmed Mutagenesis Is a Universal Model of Computation....Pages 300-307
Horn Clause Computation by Self-assembly of DNA Molecules....Pages 308-320
DNA-based Parallel Computation of Simple Arithmetic....Pages 321-328
On P Systems with Global Rules....Pages 329-339
Computing with Membranes: Variants with an Enhanced Membrane Handling....Pages 340-349
Towards an Electronic Implementation of Membrane Computing: A Formal Description of Non-deterministic Evolution in Transition P Systems....Pages 350-359
Insertion-Deletion P Systems....Pages 360-370
A Universal Time-Varying Distributed H System of Degree 1....Pages 371-380
A Note on Graph Splicing Languages....Pages 381-390
Back Matter....Pages 391-392
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