Nanotechnology: Science and Computation

Part I DNA Nanotechnology – Algorithmic Self-assembly Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks Paul W.K. Rothemund. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 A Fresh Look at DNA Nanotechnology Zhaoxiang Deng, Yi Chen, Ye Tian, Chengde Mao . . . . . . . . . . . . . . . . . . . 23 DNA Nanotechnology: an Evolving Field Hao Yan, Yan Liu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Self-healing Tile Sets Erik Winfree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Compact Error-Resilient Computational DNA Tilings John H. Reif, Sudheer Sahu, Peng Yin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Forbidding−Enforcing Conditions in DNA Self-assembly of Graphs Giuditta Franco, Nataˇsa Jonoska . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 Part II Codes for DNA Nanotechnology Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set Mirela Andronescu, Anne Condon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Involution Solid Codes Lila Kari, Kalpana Mahalingam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 X Contents Test Tube Selection of Large Independent Sets of DNA Oligonucleotides Russell Deaton, Junghuei Chen, Jin-Woo Kim, Max H. Garzon, David H. Wood . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Part III DNA Nanodevices DNA-Based Motor Work at Bell Laboratories Bernard Yurke . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 Nanoscale Molecular Transport by Synthetic DNA Machines1 Jong-Shik Shin, Niles A. Pierce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175 Part IV Electronics, Nanowire and DNA A Supramolecular Approach to Metal Array Programming Using Artificial DNA Mitsuhiko Shionoya . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191 Multicomponent Assemblies Including Long DNA and Nanoparticles – An Answer for the Integration Problem? Andreas Wolff, Andrea Csaki, Wolfgang Fritzsche . . . . . . . . . . . . . . . . . . . . 199 Molecular Electronics: from Physics to Computing Yongqiang Xue, Mark A. Ratner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Part V Other Bio-molecules in Self-assembly Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials Bruno Samor`ı, Giampaolo Zuccheri, Anita Scipioni, Pasquale De Santis 249 Adding Functionality to DNA Arrays: the Development of Semisynthetic DNA–Protein Conjugates Christof M. Niemeyer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 Bacterial Surface Layer Proteins: a Simple but Versatile Biological Self-assembly System in Nature Dietmar Pum, Margit S´ara, Bernhard Schuster, Uwe B. Sleytr . . . . . . . . . 277 1 Adapted with permission (Table 1, Figs 1–3, and associated text) from J. Am. Chem. Soc. 2004, 126, 10834–10835. Copyright 2004 American Chemical Society. Contents XI Part VI Biomolecular Computational Models Computing with Hairpins and Secondary Structures of DNA Masami Hagiya, Satsuki Yaegashi, Keiichiro Takahashi . . . . . . . . . . . . . . . 293 Bottom-up Approach to Complex Molecular Behavior Milan N. Stojanovic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309 Aqueous Computing: Writing on Molecules Dissolved in Water Tom Head, Susannah Gal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Part VII Computations Inspired by Cells Turing Machines with Cells on the Tape Francesco Bernardini, Marian Gheorghe, Natalio Krasnogor, Gheorghe P˘aun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335 Insights into a Biological Computer: Detangling Scrambled Genes in Ciliates Andre R.O. Cavalcanti, Laura F. Landweber . . . . . . . . . . . . . . . . . . . . . . . . . 349 Modelling Simple Operations for Gene Assembly Tero Harju, Ion Petre, Grzegorz Rozenberg . . . . . . . . . . . . . . . . . . . . . . . . . 361 Part VIII Appendix Publications by Nadrian C. Seeman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .