Dna Computing: 12th International Meeting On Dna Computing, Dna 12, Seoul, Korea, June 5-9, 2006 : Revised Selected Papers 12th International Meeting On Dna Computing Twelfth International Meeting On Dna Computing International Meeting On Dna Computing Dn

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. Computing With Spiking Neural P Systems : Traces And Small Universal Systems / Mihai Ionescu, Andrei Paun, Gheorghe Paun And Mario J. Perez-jimenez -- Minimal Parallelism For Polarizationless P Systems / Tseren-onolt Ishdorj -- P Systems With Active Membranes Characterize Pspace / Petr Sosik And Alfonso Rodriguez-paton -- All Np-problems Can Be Solved In Polynomial Time By Accepting Networks Of Splicing Processors Of Constant Size / Florin Manea, Carlos Martin-vide And Victor Mitrana -- Length-separating Test Tube Systems / Erzsebet Csuhaj-varju And Sergey Verlan -- Gene Assembly Algorithms For Ciliates / Lucian Ilie And Roberto Solis-oba -- Spectrum Of A Pot For Dna Complexes / Natasa Jonoska, Gregory L. Mccolm And Ana Staninska -- On The Complexity Of Graph Self-assembly In Accretive Systems / Stanislav Angelov, Sanjeev Khanna And Mirko Visontai -- Viral Genome Compression / Lucian Ilie, Liviu Tinta, Cristian Popescu And Kathleen A. Hill -- Dna Codes And Their Properties / Lila Kari And Kalpana Mahalingam -- In Search Of Optimal Codes For Dna Computing / Max H. Garzon, Vinhthuy Phan, Sujoy Roy And Andrew J. Neel -- Dna Sequence Design By Dynamic Neighborhood Searches / Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane And Masafumi Yamashita -- Sequence Design For Stable Dna Tiles / Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda And Azuma Ohuchi -- Hairpin Structures Defined By Dna Trajectories / Michael Domaratzki -- Design And Simulation Of Self-repairing Dna Lattices / Urmi Majumder, Sudheer Sahu, Thomas H. Labean And John H. Reif -- On Times To Compute Shapes In 2d Tile Self-assembly / Yuliy Baryshnikov, Ed Coffman And Boonsit Yimwadsana -- Capabilities And Limits Of Compact Error Resilience Methods For Algorithmic Self-assembly In Two And Three Dimensions / Sudheer Sahu And John H. Reif -- A Mathematical Approach To Cross-linked Structures In Viral Capsids : Predicting The Architecture Of Novel Containers For Drug Delivery / Thomas Keef -- A Framework For Modeling Dna Based Molecular Systems / Sudheer Sahu, Bei Wang And John H. Reif -- Uniquimer : A De Novo Dna Sequence Generation Computer Software For Dna Self-assembly / Bryan Wei, Zhengyu Wang And Yongli Mi -- A Probabilistic Model Of The Dna Conformational Change / Masashi Shiozaki, Hirotaka Ono, Kunihiko Sadakane And Masafumi Yamashita -- Simulations Of Microreactors : The Order Of Things / Joseph Ibershoff, Jerzy W. Jaromczyk And Danny Van Noort -- Dna Hypernetworks For Information Storage And Retrieval / Byoung-tak Zhang And Joo-kyung Kim -- Abstraction Layers For Scalable Microfluidic Biocomputers / William Thies, John Paul Urbanski, Todd Thorsen And Saman Amarasinghe -- Fuzzy Forecasting With Dna Computing / Don Jyh-fu Jeng, Junzo Watada, Berlin Wu And Jui-yu Wu -- Reasoning And Talking Dna : Can Dna Understand English? / Kiran C. Bobba, Andrew J. Neel, Vinhthuy Phan And Max H. Garzon -- A New Readout Approach In Dna Computing Based On Real-time Pcr With Taqman Probes / Zuwairie Ibrahim, John A. Rose, Yusei Tsuboi, Osamu Ono And Marzuki Khalid -- Automating The Dna Computer : Solving N-variable 3-sat Problems / Clifford R. Johnson -- Local Area Manipulation Of Dna Molecules For Photonic Dna Memory / Rui Shogenji, Naoya Tate, Taro Beppu, Yusuke Ogura And Jun Tanida -- Unravel Four Hairpins! / Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Satsuki Yaegashi And Masami Hagiya -- Displacement Whiplash Pcr : Optimized Architecture And Experimental Validation / John A. Rose, Ken Komiya, Satsuki Yaegashi And Masami Hagiya -- Methylogic : Implementation Of Boolean Logic Using Dna Methylation / Nevenka Dimitrova And Susannah Gal -- Development Of Dna Relational Database And Data Manipulation Experiments / Masahito Yamamoto, Yutaka Kita, Satoshi Kashiwamura, Atsushi Kameda And Azuma Ohuchi -- Experimental Validation Of The Statistical Thermodynamic Model For Prediction Of The Behavior Of Autonomous Molecular Computers Based On Dna Hairpin Formation / Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama And John A. Rose. Chengde Mao, Takashi Yokomori (eds.). Includes Bibliographical References And Index. Front Matter....Pages - Computing with Spiking Neural P Systems: Traces and Small Universal Systems....Pages 1-16 Minimal Parallelism for Polarizationless P Systems....Pages 17-32 P Systems with Active Membranes Characterize PSPACE....Pages 33-46 All NP-Problems Can Be Solved in Polynomial Time by Accepting Networks of Splicing Processors of Constant Size....Pages 47-57 Length-Separating Test Tube Systems....Pages 58-70 Gene Assembly Algorithms for Ciliates....Pages 71-82 Spectrum of a Pot for DNA Complexes....Pages 83-94 On the Complexity of Graph Self-assembly in Accretive Systems....Pages 95-110 Viral Genome Compression....Pages 111-126 DNA Codes and Their Properties....Pages 127-142 In Search of Optimal Codes for DNA Computing....Pages 143-156 DNA Sequence Design by Dynamic Neighborhood Searches....Pages 157-171 Sequence Design for Stable DNA Tiles....Pages 172-181 Hairpin Structures Defined by DNA Trajectories....Pages 182-194 Design and Simulation of Self-repairing DNA Lattices....Pages 195-214 On Times to Compute Shapes in 2D Tile Self-assembly....Pages 215-222 Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-assembly in Two and Three Dimensions....Pages 223-238 A Mathematical Approach to Cross-Linked Structures in Viral Capsids: Predicting the Architecture of Novel Containers for Drug Delivery....Pages 239-249 A Framework for Modeling DNA Based Molecular Systems....Pages 250-265 Uniquimer: A de Novo DNA Sequence Generation Computer Software for DNA Self-assembly....Pages 266-273 A Probabilistic Model of the DNA Conformational Change....Pages 274-285 Simulations of Microreactors: The Order of Things....Pages 286-297 DNA Hypernetworks for Information Storage and Retrieval....Pages 298-307 Abstraction Layers for Scalable Microfluidic Biocomputers....Pages 308-323 Fuzzy Forecasting with DNA Computing....Pages 324-336 “Reasoning” and “Talking” DNA: Can DNA Understand English?....Pages 337-349 A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes....Pages 350-359 Automating the DNA Computer: Solving n-Variable 3-SAT Problems....Pages 360-373 Local Area Manipulation of DNA Molecules for Photonic DNA Memory....Pages 374-380 Unravel Four Hairpins!....Pages 381-392 Displacement Whiplash PCR: Optimized Architecture and Experimental Validation....Pages 393-403 MethyLogic: Implementation of Boolean Logic Using DNA Methylation....Pages 404-417 Development of DNA Relational Database and Data Manipulation Experiments....Pages 418-427 Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation....Pages 428-438 Back Matter....Pages - This book constitutes the thoroughly refereed postproceedings of the 12th International Meeting on DNA Computing, DNA12, held in Seoul, Korea in June 2006. The 34 revised full papers presented are organized in topical sections on molecular and membrane computing models, complexity analysis, sequence and tile designs and their properties, DNA tile self-assembly models, simulator and software for DNA computing, DNA computing algorithms and new applications, novel experimental approaches, and experimental solutions. Constitutes the refereed postproceedings of the 12th International Meeting on DNA Computing, DNA12, that was held in Seoul, Korea in June 2006. This book presents 34 revised full papers that are organized in topical sections on molecular and membrane computing models, complexity analysis, sequence and tile designs and their properties, and more.