LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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236 Nataˇsa Jonoska, Shiping Liao, and Nadrian C. Seeman Fig. 11. with double-triangle double diamonds. The computational set-up is illustrated schematically in Figure 13 with just two computational tiles made of DNA triple crossover (TX) molecules. Fig. 12. Linear array of a series of devices to set-up the input. Both diamonds and trapezoids are the result of edge-sharing motifs [27]. A key difference between this structure and the previous one is that the devices between the two illustrated double diamond structures differ from each other. Consequently, we can set the states of the two devices independently. The doublediamond structures contain domains that can bind to DX molecules; this design will set up the linear array of the input, see Figure 12. Depending on the state of the devices, one or the other of the double diamonds will be on the top side. The two DX molecules will then act similarly to bind with computational TX molecules, in the gap between them, as shown schematically in Figure 13. The system is designed to be asymmetric by allowing an extra diamond for the “start” and the “end” tiles (this is necessary in order to distinguish the top and
start tile Transducers with Programmable Input by DNA Self-assembly 237 computation tile a’ b’ S0 S0 TX S1 S1 TX S2 a a b b 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 b input symbol 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 00000000 11111111 input 00000000 11111111 00000000 11111111 00000000 11111111 a PX−JX device 2 000000000 111111111 000000000 111111111 000000000 111111111 000000000 111111111 000000000 111111111 000000000 111111111 000000000 111111111 000000000 111111111 b Fig. 13. Schematic view for a couple of first step computations. The linear array of DX and TX molecules that sets up the input is substituted only with a rectangle for each of the input symbol. Fig. 14. the bottom by in atomic force microscopy, (AFM) visualizations). The left side must contain an initiator (shown blunt at the top) and the right side will contain a terminator. The bottom assembly can be removed using the same Yurke-type techniques [28] that are used to control the state of the devices for removal of the set strands. Successive layers can be added to the device by binding to the initiator on the left, and to the terminator on the right. For this task, we have prototyped the assembly of the central 4-diamond patterns, connecting them with sticky ends, rather than PX-JX2 devices. AFM images of these strings are shown on the left in Figure 14. We have also built a 5-diamond system connected by devices. Its AFM pattern is shown on the right in Figure 14. a
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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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DNA-based Cryptography Ashish Gehan
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DNA-based Cryptography 169 concern.
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DNA-based Cryptography 171 The one-
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DNA-based Cryptography 173 of DNA t
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DNA-based Cryptography 175 Fig. 3.
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DNA-based Cryptography 177 the comp
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DNA-based Cryptography 179 can be c
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DNA-based Cryptography 181 4.4 DNA-
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DNA-based Cryptography 183 Fig. 7.
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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 227 and 228: n-Insertion on Languages 217 Theore
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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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LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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