186 Ashish Gehani, Thomas LaBean, and John Reif 12. S. Fodor, J.L. Read, M.C. Pirrung, L. Stryer, A. Tsai Lu, and D. Solas, Lightdirected spatially addressable parallel chemical synthesis, Science, 251 (1991), 767–773. 13. A.G. Frutos, A.J. Thiel, A.E. Condon, L.M. Smith, and R.M. Corn, DNA <strong>Computing</strong> at Surfaces: 4 Base Mismatch Word Design, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 238. 14. J.M. Gray, T.G. Frutos, A. Michael Berman, A.E. Condon, M.G. Lagally, L.M. Smith, and R.M. Corn, Reducing Errors in DNA <strong>Computing</strong> by Appropriate Word Design, November, 1996. 15. S. Grumbach and F. Tahi, A new challenge for compression algorithms: genetic sequences, Inf. Proc. and Management, 30, 6 (1994), 875–886. 16. F. Guarnieri, M. Fliss, and C. Bancr<strong>of</strong>t, Making DNA Add, Science, 273 (1996), 220–223. 17. V. Gupta, S. Parthasarathy, and M.J. Zaki, Arithmetic and Logic Operations with DNA, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 212–220. 18. M. Hagiya, M. Arita, D. Kiga, K. Sakamoto, and S. Yokoyama, Towards Parallel Evaluation and Learning <strong>of</strong> Boolean µ-Formulas with Molecules, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 105–114. 19. T. Head, Splicing schemes and DNA, Lindenmayer Systems; Impact on Theoretical computer science and developmental biology (G. Rozenberg and A. Salomaa, eds.), Springer Verlag, Berlin, 1992, 371–383. 20. S. Henik<strong>of</strong>f and J. G. Henik<strong>of</strong>f, Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci., 89 (1992), 10915–10919. 21. D. Kahn, The Codebreakers, Macmillan, NY, 1967. 22. J.P. Klein, T.H. Leete, and H. Rubin, A biomolecular implementation <strong>of</strong> logical reversible computation with minimal energy dissipation, Proceedings 4th DIMACS Workshop on DNA Based Computers, University <strong>of</strong> Pennysylvania, Philadelphia, 1998 (L. Kari, H. Rubin, and D.H. Wood, eds.), 15–23. 23. M. Kotera, A.G. Bourdat, E. Defrancq, and J. Lhomme, A highly efficient synthesis <strong>of</strong> oligodeoxyribonucleotides containing the 2’-deoxyribonolactone lesion, J. Am. Chem. Soc., 120 (1998), 11810–11811. 24. T.H. LaBean and T.R. Butt, Methods and materials for producing gene libraries, U.S. Patent Number 5,656,467, 1997. 25. T. LaBean and S.A. Kauffman, Design <strong>of</strong> synthetic gene libraries encoding random sequence proteins with desired ensemble characteristics, Protein Science, 2 (1993), 1249–1254. 26. T.H. LaBean, E. Winfree, and J.H. Reif, Experimental Progress in Computation by Self-Assembly <strong>of</strong> DNA Tilings, DNA Based Computers V, 1999. 27. T.H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, H.J. Reif, and N C. Seeman, The construction, analysis, ligation and self-assembly <strong>of</strong> DNA triple crossover complexes, J. Am. Chem. Soc., 122 (2000), 1848–1860. 28. X. Li, X. Yang, J. Qi, and N.C. Seeman, Antiparallel DNA double crossover molecules as components for nanoconstruction, J. Amer. Chem. Soc., 118 (1996), 6131–6140. 29. Loewenstern and Yianilos, Significantly Lower Entropy Estimates for Natural DNA Sequences, DCC: Data Compression Conference, IEEE Computer Society TCC, (1997), 151–161.
DNA-based Cryptography 187 30. C. Mao, T.H. LaBean, J.H. Reif, and N C. Seeman, Logical computation using algorithmic self-assembly <strong>of</strong> DNA triple-crossover molecules, Nature, 407 (2000), 493–496. 31. A.P. Mills Jr., B. Yurke, and P.M. Platzman, Article for analog vector algebra computation, Proceedings 4th DIMACS Workshop on DNA Based Computers, University <strong>of</strong> Pennysylvania, Philadelphia, 1998 (L. Kari, H. Rubin, and D.H. Wood, eds.), 175–180. 32. K.U. Mir, A Restricted Genetic Alphabet for DNA <strong>Computing</strong>, Proceedings <strong>of</strong> the Second Annual Meeting on DNA Based Computers, Princeton University, 1996, in DNA based computer II (Editors:L.Landwaber,E.Baum)DIMACSseriesin Discrete Math. and Theoretical Comp. Sci. 44 (1999). 33. C.G. Nevill-Manning and I.H. Witten, Protein is Incompressible, IEEE Data Compression Conference, IEEE Computer Society TCC, 1999, 257–266. 34. M. Orlian, F. Guarnieri, and C. Bancr<strong>of</strong>t, Parallel Primer Extension Horizontal Chain Reactions as a Paradigm <strong>of</strong> Parallel DNA-Based Computation, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 142–158. 35. A.C. Pease, D. Solas, E.J. Sullivan, M.T. Cronin, C.P. Holmes, and S. P. Fodor, Light-generated oligonucleotide arrays for rapid DNA sequence analysis, Proc. Natl Acad. Sci. USA, 91 (1994), 5022–5026. 36. J.H. Reif, Local Parallel Biomolecular <strong>Computing</strong>, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 243–264. 37. J.H. Reif, Paradigms for Biomolecular Computation, Unconventional Models <strong>of</strong> Computation (C.S. Calude, J. Casti, and M.J. Dinneen, eds.), Springer, 1998. 38. J.H. Reif, Parallel <strong>Molecular</strong> Computation: Models and Simulations, Algorithmica, Special Issue on Computational Biology, 1998. 39. S.S. Roberts, Turbocharged PCR, Jour. <strong>of</strong> N.I.H. Research, 6 (1994), 46–82. 40. J.A. Rose, R. Deaton, M. Garzon, R.C. Murphy, D.R. Franceschetti, and S.E. Stevens Jr., The effect <strong>of</strong> uniform melting temperatures on the efficiency <strong>of</strong> DNA computing, DNA based computer III (Editors: H. Rubin, D. Wood) DIMACS series in Discrete Math. and Theoretical Comp. Sci. vol 48 (1999) 35–42. 41. S. Roweis, E. Winfree, R. Burgoyne, N.V. Chelyapov, M.F. Goodman, P.W.K. Rothemund, and L.M. Adleman, A Sticker Based Architecture for DNA Computation, DNA based computer II (Editors: L. Landwaber, E. Baum) DIMACS series in Discrete Math. and Theoretical Comp. Sci. 44 (1999) 1-29. 42. B. Schneier, Applied Cryptography: Protocols, Algorithms, and Source Code in C, John Wiley & Sons, Inc., 1996. 43. J.A. Storer, Data Compression: Methods and Theory, Computer Science Press, 1988. 44. A. Suyama, DNA chips - Integrated Chemical Circuits for DNA Diagnosis and DNA computers, 1998. 45. C.T. Taylor, V. Risca, and C. Bancr<strong>of</strong>t, Hiding messages in DNA microdots, Nature, 399 (1999), 533–534. 46. E. Winfree, On the Computational Power <strong>of</strong> DNA Annealing and Ligation, DNA Based Computers (E.B. Baum and R.J. Lipton, eds.), American Mathematical Society, DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, 1995, 187–198. 47. E. Winfree, Complexity <strong>of</strong> Restricted and Unrestricted Models <strong>of</strong> <strong>Molecular</strong> Computation, DNA Based Computers (E.B. Baum and R.J. Lipton, eds.), American
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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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Solving Graph Problems by P Systems
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Solving Graph Problems by P Systems
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Solving Graph Problems by P Systems
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Solving Graph Problems by P Systems
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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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Solving Graph Problems by P Systems
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Solving Graph Problems by P Systems
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Solving Graph Problems by P Systems
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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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Balance Machines: Computing = Balan
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Balance Machines: Computing = Balan
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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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Eilenberg P Systems with Symbol-Obj
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Eilenberg P Systems with Symbol-Obj
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Eilenberg P Systems with Symbol-Obj
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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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Molecular Tiling and DNA Self-assem
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Molecular Tiling and DNA Self-assem
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Molecular Tiling and DNA Self-assem
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Molecular Tiling and DNA Self-assem
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Molecular Tiling and DNA Self-assem
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8 Hierarchical Tiling Molecular Til
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Molecular Tiling and DNA Self-assem
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Molecular Tiling and DNA Self-assem
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References Molecular Tiling and DNA
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Molecular Tiling and DNA Self-assem
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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On Some Classes of Splicing Languag
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ˆxa ˆby ✬ ✩✬ ✩ a b x y
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On Some Classes of Splicing Languag
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The Power of Networks of Watson-Cri
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The Power of Networks of Watson-Cri
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The Power of Networks of Watson-Cri
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The Power of Networks of Watson-Cri
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The Power of Networks of Watson-Cri
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The Power of Networks of Watson-Cri
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Fixed Point Approach to Commutation
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Fixed Point Approach to Commutation
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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 Approach to Commutation
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� � � � � Fixed Point App
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Fixed Point Approach to Commutation
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Remarks on Relativisations and DNA
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start tile Transducers with Program
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Transducers with Programmable Input
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Methods for Constructing Coded DNA
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Methods for Constructing Coded DNA
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u u Methods for Constructing Coded
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Methods for Constructing Coded DNA
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Methods for Constructing Coded DNA
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Methods for Constructing Coded DNA
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Methods for Constructing Coded DNA
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On the Universality of P Systems wi
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On the Universality of P Systems wi
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On the Universality of P Systems wi
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On the Universality of P Systems wi
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On the Universality of P Systems wi
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On the Universality of P Systems wi
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An Algorithm for Testing Structure
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An Algorithm for Testing Structure
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An Algorithm for Testing Structure
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An Algorithm for Testing Structure
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An Algorithm for Testing Structure
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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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A DNA Algorithm for the Hamiltonian
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A DNA Algorithm for the Hamiltonian
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A DNA Algorithm for the Hamiltonian
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Formal Languages Arising from Gene
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Formal Languages Arising from Gene
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Formal Languages Arising from Gene
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Formal Languages Arising from Gene
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Formal Languages Arising from Gene
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Formal Languages Arising from Gene
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A Proof of Regularity for Finite Sp
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A Proof of Regularity for Finite Sp
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A Proof of Regularity for Finite Sp
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--- ◦ ❄ ⊗ γ ✲ A Proof of R
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A Proof of Regularity for Finite Sp
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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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Membrane Computing: Some Non-standa
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Membrane Computing: Some Non-standa
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Membrane Computing: Some Non-standa
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Membrane Computing: Some Non-standa
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Membrane Computing: Some Non-standa
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The P Versus NP Problem Through Cel
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The P Versus NP Problem Through Cel
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The P Versus NP Problem Through Cel
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The P Versus NP Problem Through Cel
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The P Versus NP Problem Through Cel
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The P Versus NP Problem Through Cel
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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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Communicating Distributed H Systems
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Communicating Distributed H Systems
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Proof Communicating Distributed H S
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Communicating Distributed H Systems
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Communicating Distributed H Systems
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Communicating Distributed H Systems
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Communicating Distributed H Systems
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Communicating Distributed H Systems
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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