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9783540341611

DNA Computing

by ; ;
  • ISBN13:

    9783540341611

  • ISBN10:

    3540341617

  • Edition: 1st
  • Format: Paperback
  • Copyright: 2006-09-30
  • Publisher: Springer-Verlag New York Inc
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Supplemental Materials

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Summary

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.

Table of Contents

Self-correcting Self-assembly: Growth Models and the Hammersley Process
Yuliy Baryshnikov, Ed Coffman, Nadrian Seeman, Teddy Yimwadsana
1(11)
Recognizing DNA Splicing
Matteo Cavaliere, Nataša Jonoska, Peter Leupold
12(15)
On Computational Properties of Template-Guided DNA Recombination
Mark Daley, Ian McQuillan
27(11)
Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks
Joseph Farfel, Darko Stefanovic
38(17)
DNA Recombination by XPCR
Giuditta Franco, Vincenzo Manca, Cinzia Giagulli, Carlo Laudanna
55(12)
An Algorithm for SAT Without an Extraction Phase
Pierluigi Frisco, Christiaan Henkel, Szabolcs Tengely
67(14)
Sensitivity and Capacity of Microarray Encodings
Max H. Garzon, Vinhthuy Phan, Kiran C. Bobba, Raghuver Kontham
81(15)
Simple Operations for Gene Assembly
Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg
96(16)
Counting Time in Computing with Cells
Oscar H. Ibarra, Andrei Paun
112(17)
On Bounded Symport/Antiport P Systems
Oscar H. Ibarra, Sara Woodworth
129(15)
Expectation and Variance of Self-assembled Graph Structures
Nataša Jonoska, Gregory L. McColm, Ana Staninska
144(14)
Hairpin Structures in DNA Words
Lila Kari, Stavros Konstantinidis, Elena Losseva, Petr Sosik, Gabriel Thierrin
158(13)
Efficient Algorithm for Testing Structure Freeness of Finite Set of Biomolecular Sequences
Atsushi Kijima, Satoshi Kobayashi
171(10)
Communicating Distributed H Systems: Optimal Results with Efficient Ways of Communication
Shankara Narayanan Krishna
181(12)
Intensive In Vitro Experiments of Implementing and Executing Finite Automata in Test Tube
Junna Kuramochi, Yasubumi Sakakibara
193(10)
Development of an In Vivo Computer Based on Escherichia coli
Hirotaka Nakagawa, Kensaku Sakamoto, Yasubumi Sakakibara
203(10)
Control of DNA Molecules on a Microscopic Bead Using Optical Techniques for Photonic DNA Memory
Yusuke Ogura, Taro Beppu, Masahiro Takinoue, Akira Suyama, Jun Tanida
213(11)
Linearizer and Doubler: Two Mappings to Unify Molecular Computing Models Based on DNA Complementarity
Kaoru Onodera, Takashi Yokomori
224(12)
Analysis and Simulation of Dynamics in Probabilistic P Systems
Dario Pescini, Daniela Besozzi, Claudio Zandron, Giancarlo Mauri
236(12)
Experimental Validation of DNA Sequences for DNA Computing: Use of a SYBR Green I Assay
Wendy K. Pogozelski, Matthew P. Bernard, Salvatore F. Priore, Anthony J. Macula
248(9)
Complexity of Graph Self-assembly in Accretive Systems and Self-destructible Systems
John H. Reif, Sudheer Sahu, Peng Yin
257(18)
Designing Nucleotide Sequences for Computation: A Survey of Constraints
Jennifer Sager, Darko Stefanovic
275(15)
A Self-assembly Model of Time-Dependent Glue Strength
Sudheer Sahu, Peng Yin, John H. Reif
290(15)
Complexity of Compact Proofreading for Self-assembled Patterns
David Soloveichik, Erik Winfree
305(20)
A Microfluidic Device for DNA Tile Self-assembly
Koutaro Somei, Shohei Kaneda, Teruo Fujii, Satoshi Murata
325(11)
Photo- and Thermoregulation of DNA Nanomachines
Keiichiro Takahashi, Satsuki Yaegashi, Hiroyuki Asanuma, Masami Hagiya
336(11)
Chain Reaction Systems Based on Loop Dissociation of DNA
Keiichiro Takahashi, Satsuki Yaegashi, Atsushi Kameda, Masami Hagiya
347(12)
A Local Search Based Barrier Height Estimation Algorithm for DNA Molecular Transitions
Tsutomu Takeda, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita
359(12)
Specificity of Hybridization Between DNA Sequences Based on Free Energy
Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
371(9)
A Poor Man's Microfluidic DNA Computer
Danny van Noort
380(7)
Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences
Bei Wang, Dimitris Papamichail, Steffen Mueller, Steven Skiena
387(12)
Design of Autonomous DNA Cellular Automata
Peng Yin, Sudheer Sahu, Andrew J. Turberfield, John H. Reif
399(18)
Use of DNA Nanodevices in Modulating the Mechanical Properties of Polyacrylamide Gels
Bernard Yurke, David C. Lin, Noshir A. Langrana
417(10)
Molecular Learning of wDNF Formulae
Byoung-Tak Zhang, Ha-Young Jang
427(12)
Author Index 439

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