LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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218 Masami Ito and Ryo Sugiura 5. L. Kari, Gh. Păun, G. Thierrin, S. Yu, At the crossroads of DNA computing and formal languages: Characterizing RE using insertion-deletion systems, Prof. 3rd DI- MACS Workshop on DNA Based Computers, Philadelphia, 1997, 318–333. 6. Gh. Păun, G. Rozenberg, A. Salomaa, DNA Computing. New Computing Paradigms, Springer, Berlin, 1998.
Transducers with Programmable Input by DNA Self-assembly Nataˇsa Jonoska 1 , Shiping Liao 2 , and Nadrian C. Seeman 2 1 University of South Florida, Department of Mathematics Tampa, FL 33620, USA jonoska@math.usf.edu 2 New York University, Department of Chemistry New York, NY 1003, USA sl558@nyu.edu, ned.seeman@nyu.edu Abstract. Notions of Wang tiles, finite state machines and recursive functions are tied together. We show that there is a natural way to simulate finite state machines with output (transducers) with Wang tiles and we show that recursive (computable) functions can be obtained as composition of transducers through employing Wang tiles. We also show how a programmable transducer can be self-assembled using TX DNA molecules simulating Wang tiles and a linear array of DNA PX-JX2 nanodevices. 1 Introduction In recent years there have been several major developments both experimentally and theoretically, that use DNA for obtaining three dimensional nanostructures, computation and as a material for nano-devices. Nanostructures. The inherently informational character of DNA makes it an attractive molecule for use in applications that entail targeted assembly. Genetic engineers have used the specificity of sticky-ended cohesion to direct the construction of plasmids and other vectors. Naturally-occurring DNA is a linear molecule in the sense that its helix axis is a line, although that line is typically not straight. Linear DNA molecules are not well-suited to serve as components of complex nanomaterials, but it is easy to construct DNA molecules with stable branch points [20]. Synthetic molecules have been designed and shown to assemble into branched species [12,23], and more complex species that entail the lateral fusion of DNA double helices [21], such as DNA double crossover (DX) molecules [7], triple crossover (TX) molecules [13] or paranemic crossover (PX) molecules. Double and triple cross-over molecules have been used as tiles and building blocks for large nanoscale arrays [24,25]. In addition, three dimensional structures such as a cube [4], a truncated octahedron [29] and arbitrary graphs [10,19] have been constructed from DNA duplex and junction molecules. Computation. Theoretically, it has been shown that two dimensional arrays can simulate the dynamics of a bounded one dimensional cellular automaton and so are capable of potentially performing computations as a Universal Turing N. Jonoska et al. (Eds.): Molecular Computing (Head Festschrift), LNCS 2950, pp. 219–240, 2004. c○ Springer-Verlag Berlin Heidelberg 2004
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Lecture Notes in Computer Science 2
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Nata˘sa Jonoska Gheorghe Păun Grz
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Thomas J. Head
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VIII Preface portant to keep in min
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X Table of Contents Formal Properti
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Solving Graph Problems by P Systems
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where Solving Graph Problems by P S
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Writing Information into DNA Masano
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Writing Information into DNA 25 Ham
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Writing Information into DNA 27 Fig
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Writing Information into DNA 29 Dea
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5 Results 5.1 DNA Code for the Engl
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Writing Information into DNA 33 3.
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Writing Information into DNA 35 101
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Balance Machines: Computing = Balan
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+ .. . + Balance Machines: Computin
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x Balance Machines: Computing = Bal
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1 Balance Machines: Computing = Bal
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Eilenberg P Systems with Symbol-Obj
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2 Definitions Definition 1. A strea
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5 Conclusions Eilenberg P Systems w
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Molecular Tiling and DNA Self-assem
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3 Molecular Self-assembly Processes
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8 Hierarchical Tiling Molecular Til
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References Molecular Tiling and DNA
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On Some Classes of Splicing Languag
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ˆxa ˆby ✬ ✩✬ ✩ a b x y
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The Power of Networks of Watson-Cri
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Fixed Point Approach to Commutation
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Here the last one holds if and only
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� � � � � Fixed Point App
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Remarks on Relativisations and DNA
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Splicing Test Tube Systems and Thei
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Splicing Test Tube Systems 141 the
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Splicing Test Tube Systems 143 to a
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Splicing Test Tube Systems 145 6. R
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Splicing Test Tube Systems 147 (c)
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I0 Ai i Splicing Test Tube Systems
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Splicing Test Tube Systems 151 4. J
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Digital Information Encoding on DNA
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Page 177 and 178: DNA-based Cryptography Ashish Gehan
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Page 185 and 186: DNA-based Cryptography 175 Fig. 3.
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Page 197 and 198: DNA-based Cryptography 187 30. C. M
Page 199 and 200: Splicing to the Limit Elizabeth Goo
Page 201 and 202: Splicing to the Limit 191 molecular
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Page 211 and 212: 6 Conclusion Splicing to the Limit
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Page 223 and 224: n-Insertion on Languages Masami Ito
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Page 227: n-Insertion on Languages 217 Theore
Page 231 and 232: Transducers with Programmable Input
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An Algorithm for Testing Structure
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Definition 1. Define the relation
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280 Manfred Kudlek Definition 5. Co
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On Languages of Cyclic Words 283 Th
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On Languages of Cyclic Words 285 No
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On Languages of Cyclic Words 287 Th
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A DNA Algorithm for the Hamiltonian
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Formal Languages Arising from Gene
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A Proof of Regularity for Finite Sp
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--- ◦ ❄ ⊗ γ ✲ A Proof of R
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The Duality of Patterning in Molecu
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The Duality of Patterning in Molecu
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Membrane Computing: Some Non-standa
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where: Membrane Computing: Some Non
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where: Membrane Computing: Some Non
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The P Versus NP Problem Through Cel
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Realizing Switching Functions Using
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Realizing Switching Functions Using
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AND Gate Realizing Switching Functi
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NOR Gate Realizing Switching Functi
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Plasmids to Solve #3SAT Rani Siromo
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Plasmids to Solve #3SAT 363 A comme
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Plasmids to Solve #3SAT 365 from th
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Communicating Distributed H Systems
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Proof Communicating Distributed H S
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Books: Publications by Thomas J. He
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Publications by Thomas J. Head 387
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Publications by Thomas J. Head 389
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