LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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166 Max H. Garzon, Kiranchand V. Bobba, and Bryan P. Hyde 22. T. Head, M. Yamamura, S. Gal (1999), Aqueous Computing: Writing on Molecules. Proceedings of the Congress on Evolutionary Computing (CEC’99). 23. T. Head (1986), Formal Language Thery and DNA; An Analysis of the Generative Capacity of Specific Recombinant Behaviors. Bull. of Mathematical Biology 49:6, 737-759. 24. N. Jonoska, N. Seeman, eds. (2001), Proc. 7th Int. Workshop on DNA-Based Computers DNA 2000, Tampa, Florida. Lecture Notes in Computer Science LNCS 2340, Springer-Verlag, 2002. 25. J.R. Koza, K. Deb, M. Dorigo, D.B. Fogel, M. Garzon, H. Iba, R.L. Riolo, eds. (1997). Proc. 2nd Annual Genetic Programming Conference. Morgan Kaufmann, San Mateo, California. 26. J. Roman (1995), The Theory of Error-Correcting Codes. Springer-Verlag, Berlin. 27. H. Rubin. D. Wood, eds. (1997), Third DIMACS Workshop on DNA-Based Computers, The University of Pennsylvania, 1997. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Providence, RI: American Mathematical Society 48 (1999). 28. J. SantaLucia, Jr., H.T. Allawi, P.A. Seneviratne (1990), Improved Nearest Neighbor Paramemeters for Predicting Duplex Stability. Biochemistry 35, 3555-3562. 29. P.W. Shor (1996), Fault-Tolerant Quantum Computation. Proc. 37th FOCS, 56-65. 30. J.G. Wetmur (1997), Physical Chemistry of Nucleic Acid Hybridization. In: [27], 1-23.
DNA-based Cryptography Ashish Gehani, Thomas LaBean, and John Reif Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA {geha,thl,reif}@cs.duke.edu Abstract. Recent research has considered DNA as a medium for ultrascale computation and for ultra-compact information storage. One potential key application is DNA-based, molecular cryptography systems. We present some procedures for DNA-based cryptography based on onetime-pads that are in principle unbreakable. Practical applications of cryptographic systems based on one-time-pads are limited in conventional electronic media by the size of the one-time-pad; however DNA provides a much more compact storage medium, and an extremely small amount of DNA suffices even for huge one-time-pads. We detail procedures for two DNA one-time-pad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pair-wise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of natural DNA or for artificial DNA encoding binary data. In the latter case, we also present a novel use of chip-based DNA micro-array technology for 2D data input and output. Finally, we examine a class of DNA steganography systems, which secretly tag the input DNA and then hide it within collections of other DNA. We consider potential limitations of these steganographic techniques, proving that in theory the message hidden with such a method can be recovered by an adversary. We also discuss various modified DNA steganography methods which appear to have improved security. 1 Introduction 1.1 Biomolecular Computation Recombinant DNA techniques have been developed for a wide class of operations on DNA and RNA strands. There has recently arisen a new area of research known as DNA computing, which makes use of recombinant DNA techniques for doing computation, surveyed in [37]. Recombinant DNA operations were shown to be theoretically sufficient for universal computation [19]. Biomolecular computing (BMC) methods have been proposed to solve difficult combinatorial search problems such as the Hamiltonian path problem [1], using the vast parallelism available to do the combinatorial search among a large number of possible solutions represented by DNA strands. For example, [5] and [41] propose BMC N. Jonoska et al. (Eds.): Molecular Computing (Head Festschrift), LNCS 2950, pp. 167–188, 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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Page 129 and 130: Fixed Point Approach to Commutation
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Page 139 and 140: � � � � � Fixed Point App
Page 143 and 144: Remarks on Relativisations and DNA
Page 149 and 150: Splicing Test Tube Systems and Thei
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Page 163 and 164: Digital Information Encoding on DNA
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Page 179 and 180: DNA-based Cryptography 169 concern.
Page 181 and 182: DNA-based Cryptography 171 The one-
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Page 185 and 186: DNA-based Cryptography 175 Fig. 3.
Page 187 and 188: DNA-based Cryptography 177 the comp
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Page 199 and 200: Splicing to the Limit Elizabeth Goo
Page 201 and 202: Splicing to the Limit 191 molecular
Page 203 and 204: Splicing to the Limit 193 Discussio
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n-Insertion on Languages 217 Theore
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Transducers with Programmable Input
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1 01 s 0 Transducers with Programma
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order β l Transducers with Program
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start tile Transducers with Program
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Methods for Constructing Coded DNA
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u u Methods for Constructing Coded
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On the Universality of P Systems wi
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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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LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

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