12. DNA 2006: Seoul, Korea

Molecular and Membrane Computing Models

• Mihai Ionescu, Andrei Paun, Gheorghe Paun, Mario J. Pérez-Jiménez:
  Computing with Spiking Neural P Systems: Traces and Small Universal Systems. 1-16
  
• Tseren-Onolt Ishdorj:
  Minimal Parallelism for Polarizationless P Systems. 17-32
  
• Petr Sosík, Alfonso Rodríguez-Patón:
  P Systems with Active Membranes Characterize PSPACE. 33-46
  
• Florin Manea, Carlos Martín-Vide, Victor Mitrana:
  All NP-Problems Can Be Solved in Polynomial Time by Accepting Networks of Splicing Processors of Constant Size. 47-57
  
• Erzsébet Csuhaj-Varjú, Sergey Verlan:
  Length-Separating Test Tube Systems. 58-70
  
• Lucian Ilie, Roberto Solis-Oba:
  Gene Assembly Algorithms for Ciliates. 71-82
  

Complexity Analysis

• Natasa Jonoska, Gregory L. McColm, Ana Staninska:
  Spectrum of a Pot for DNA Complexes. 83-94
  
• Stanislav Angelov, Sanjeev Khanna, Mirkó Visontai:
  On the Complexity of Graph Self-assembly in Accretive Systems. 95-110
  
• Lucian Ilie, Liviu Tinta, Cristian Popescu, Kathleen A. Hill:
  Viral Genome Compression. 111-126
  

Sequence and Tile Designs and Their Properties

• Lila Kari, Kalpana Mahalingam:
  DNA Codes and Their Properties. 127-142
  
• Max H. Garzon, Vinhthuy T. Phan, Sujoy Roy, Andrew Neel:
  In Search of Optimal Codes for DNA Computing. 143-156
  
• Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita:
  DNA Sequence Design by Dynamic Neighborhood Searches. 157-171
  
• Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi:
  Sequence Design for Stable DNA Tiles. 172-181
  
• Michael Domaratzki:
  Hairpin Structures Defined by DNA Trajectories. 182-194
  

DNA Tile Self-assembly Models

• Urmi Majumder, Sudheer Sahu, Thomas H. LaBean, John H. Reif:
  Design and Simulation of Self-repairing DNA Lattices. 195-214
  
• Yuliy M. Baryshnikov, Edward G. Coffman Jr., Boonsit Yimwadsana:
  On Times to Compute Shapes in 2D Tile Self-assembly. 215-222
  
• Sudheer Sahu, John H. Reif:
  Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-assembly in Two and Three Dimensions. 223-238
  
• Thomas Keef:
  A Mathematical Approach to Cross-Linked Structures in Viral Capsids: Predicting the Architecture of Novel Containers for Drug Delivery. 239-249
  

Simulator and Software for DNA Computing

• Sudheer Sahu, Bei Wang, John H. Reif:
  A Framework for Modeling DNA Based Molecular Systems. 250-265
  
• Bryan Wei, Zhengyu Wang, Yongli Mi:
  Uniquimer: A de Novo DNA Sequence Generation Computer Software for DNA Self-assembly. 266-273
  
• Masashi Shiozaki, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita:
  A Probabilistic Model of the DNA Conformational Change. 274-285
  
• Joseph Ibershoff, Jerzy W. Jaromczyk, Danny van Noort:
  Simulations of Microreactors: The Order of Things. 286-297
  

DNA Computing Algorithms and New Applications

• Byoung-Tak Zhang, Joo-Kyung Kim:
  DNA Hypernetworks for Information Storage and Retrieval. 298-307
  
• William Thies, John Paul Urbanski, Todd Thorsen, Saman P. Amarasinghe:
  Abstraction Layers for Scalable Microfluidic Biocomputers. 308-323
  
• Don Jyh-Fu Jeng, Junzo Watada, Berlin Wu, Jui-Yu Wu:
  Fuzzy Forecasting with DNA Computing. 324-336
  
• Kiranchand V. Bobba, Andrew Neel, Vinhthuy T. Phan, Max H. Garzon:
  "Reasoning" and "Talking" DNA: Can DNA Understand English? 337-349
  

Novel Experimental Approaches

• Zuwairie Ibrahim, John A. Rose, Yusei Tsuboi, Osamu Ono, Marzuki Khalid:
  A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes. 350-359
  
• Clifford R. Johnson:
  Automating the DNA Computer: Solving n-Variable 3-SAT Problems. 360-373
  
• Rui Shogenji, Naoya Tate, Taro Beppu, Yusuke Ogura, Jun Tanida:
  Local Area Manipulation of DNA Molecules for Photonic DNA Memory. 374-380
  

Experimental Solutions

• Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Satsuki Yaegashi, Masami Hagiya:
  Unravel Four Hairpins! 381-392
  
• John A. Rose, Ken Komiya, Satsuki Yaegashi, Masami Hagiya:
  Displacement Whiplash PCR: Optimized Architecture and Experimental Validation. 393-403
  
• Nevenka Dimitrova, Susannah Gal:
  MethyLogic: Implementation of Boolean Logic Using DNA Methylation. 404-417
  
• Masahito Yamamoto, Yutaka Kita, Satoshi Kashiwamura, Atsushi Kameda, Azuma Ohuchi:
  Development of DNA Relational Database and Data Manipulation Experiments. 418-427
  
• Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama, John A. Rose:
  Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation. 428-438