DNA computing : 7th International Workshop on DNA-Based Computers, DNA 7, 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. 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 Biomolecular Computing Is An Interdisciplinary ?eld That Draws Together Mol- Ular Biology, Chemistry, Physics, Computer Science, And Mathematics. Dna N- Otechnology And Molecular Biology Are Key Relevant Experimental Areas, Where Knowledge Increases With Each Passing Year. The Annual International Meeting On Dna-based Computation Has Been An Exciting Forum Where Scientists Of D- Ferent Backgrounds Who Share A Common Interest In Biomolecular Computing Meetanddiscusstheirlatestresults. Thecentralgoalofthisconeren F Ceisto Bring Together Experimentalists And Theoreticians Whose Insights Can Calibrate Each Other’s Approaches. Dna7, The Seventh International Meeting On Dna Based Computers,washeldattheuniversityofsouthfloridaintampa,fl, Usa, June 10–13,2001. The Organizerssought To Attract The Most Signi?cant - Centresearch,withthehighestimpactonthedevelopmentofthediscipline. The Meeting Had 93 Registered Participants From 14 Countries Around The World. The Program Committee Received 44 Abstracts, From Which 26 Papers Were Presented At The Meeting, And Included In This Volume. In Addition To These Papers, The Program Committee Chose 9 Additional Papers From The Poster Presentations, And Their Revised Versions Have Been Added To This Volume. As Is Now A Tradition, Four Tutorials Were Presented On The ?rst Day Of The Meeting. The Morning Started With General Tutorials By Erik Winfree (caltech) Andjunghueichen(universityofdelaware),designedtobridgebetweentheir Respectiveareasofexpertise,computerscienceandmolecularbiology. Mores- Cialized Tutorials On Encoding Dna Sequences And On Non-standard Dna Motifs And Interactions Were Given In The Afternoon By Anne Condon (university Of British Columbia) And Nadrian C. Seeman (new York University), Respectively. An Object Oriented Simulation Of Real Occurring Molecular Biological Processes For Dna Computing And Its Experimental Verification / T. Hinze, U. Hatnik And M. Sturm -- Towards Optimization Of Pcr Protocol In Dna Computing / S. Kashiwamura, M. Nakatsugawa, M. Yamamoto, T. Shiba And A. Ohuchi -- Dnasequencegenerator: A Program For The Construction Of Dna Sequences / U. Feldkamp, S. Saghafi, W. Banzhaf And H. Rauhe -- Dna Computing In Microreactors / D. Van Noort, F.-u. Gast And J.s. Mccaskill -- Cascadable Hybridisation Transfer Of Specific Dna Between Microreactor Selection Modules / R. Penchovsky And J.s. Mccaskill -- Coding Properties Of Dna Languages / S. Hussini, L. Kari And S. Konstantinidis. Nataša Jonoska, Nadrian C. Seeman (eds.). Includes Bibliographical References And Index.