14. fejezet - Ajánlott irodalom (tematikusan)

Átfogó jellegű, a DNS számítógépeket, illetve modelljeiket részletesen áttekintő könyvek:

[Amos] M. Amos: Theoretical and experimental DNA computation, Springer, 2005.

[Ignatova et al.] Ignatova, I. Martínez-Pérez, K.-H. Zimmermann: DNA computing models, Springer, New York, 2008.

[Păun et al.] Gh. Păun, G. Rozenberg, A. Salomaa: DNA Computing: New computing paradigms, Springer-Verlag, Berlin, 1998.

[Rozenberg et al.] G. Rozenberg, T. Bäck, J.N. Kok (Eds.): Handbook of Natural Computing, Springer, 2012.

És ezen belül a IV. rész (Molecular Computation), amely a következő fejezetekből áll:

[33.] L. Kari, S. Seki, P. Sosík: DNA Computing - Foundations and Implications, 1073-1127.

[34.] M. Hagiya, S. Kobayashi, K.Komiya, F. Tanaka, T. Yokomori: Molecular Computing Machineries - Computing Models and Wet Implementations, 1129-1184.

[35.] Gh. Păun: DNA Computing by Splicing and by Insertion-Deletion, 1185-1202.

[36.] Y. Sakakibara, S. Hiyama: Bacterial Computing and Molecular Communication, 1203-1232.

[37.] R. Brijder, M. Daley, T. Harju, N. Jonoska, I. Petre, G. Rozenberg: Computational Nature of Gene Assembly in Ciliates, 1233-1280.

[38.] M. Arita, M. Hagiya, M. Takinoue, F. Tanaka: DNA Memory, 1281-1318.

[39.] J.H. Reif, T.H. LaBean: Engineering Natural Computation by Autonomous DNA-Based Biomolecular Devices, 1319-1353.

[40.] Gh. Păun: Membrane Computing, 1355-1377.

A DNS szerkezetével, és a molekuláris biológiával kapcsolatban ajánljuk:

[Watson et al.] J.D. Watson, J. Tooze, D.T. Kurtz: A rekombináns DNS, Mezőgazdasági Kiadó, Budapest, 1988.

A legelső kísérleti DNS számítások a következő publikációkban kerültek közlésre:

[Adleman] L.H. Adleman: Molecular computation of solutions to combinatorial problems, Science 266 (1994), 1021-1024.

[Lipton] R.J. Lipton: DNA solution of hard computational problems, Science 268 (1995), 542-545.

További cikkek a szűrő és dominó rendszerekkel kapcsolatban:

[Halász et al.] V. Halász, L. Hegedüs, I. Hornyák, B. Nagy: Solving application oriented graph theoretical problems with DNA computing, Seventh International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA 2012), Advances in Intelligent Systems and Computing (AISC, Springer) 201 (2012), 75-85.

[Hoogeboom, Vugt] H. Hoogeboom, N. van Vugt: Fair sticker languages, Acta Informatica 37 (2000), 213-225.

[Roweis et al.] S. Roweis, E. Winfree, R. Burgoyne, N.V. Chelyapov, M.F. Goodman, P.W. K. Rothemund, L.M. Adleman: Sticker-based model for DNA computation, Journal of Computational Biology 5 (1998), 615-629.

A WK-automatákkal kapcsolatos eredmények részletei megtalálhatóak a következő művekben:

[Czeizler, Czeizler] E. Czeizler, E. Czeizler: A short survey on Watson-Crick automata, Bulletin of the EATCS 89 (2006), 104-119.

[Hegedüs et al.] L. Hegedüs, B. Nagy, Ö. Egecioglu: Stateless multicounter 5' → 3' Watson-Crick automata: The deterministic case, Natural Computing 11 (2012), 361-368.

[Herendi, Nagy] Herendi T., Nagy B.: Párhuzamos algoritmusmodellek, Typotex, Budapest, 2014.

[Kuske, Weigel] D. Kuske, P. Weigel: The role of the complementarity relation in Watson-Crick automata and sticker systems. 8th International Conference on Developments in Language Theory (DLT 2004), Lecture Notes in Computer Science (LNCS, Springer) 3340 (2004), 272-283.

[Leupold, Nagy] P. Leupold, B. Nagy: 5' → 3' Watson-Crick automata with several runs, Fundamenta Informaticae 104 (2010) 71-91.

[Nagy 2008] B. Nagy: On 5' → 3' sensing Watson-Crick finite automata, The 13th International Meeting on DNA Computing (DNA 13), Lecture Notes in Computer Science (LNCS, Springer) 4848 (2008), 256-262.

[Nagy 2013] B. Nagy: On a hierarchy of 5' → 3' sensing Watson-Crick finite automata languages, Journal of Logic and Computation (Oxford University Press) - JLC 23 (2013), 855-872.

[Onodera, Yokomori] K. Onodera, T. Yokomori: Doubler and linearizer: an approach toward a unified theory for molecular computing based on DNA complementarity, Natural Computing 7 (2008), 125-143.

[Sempere] J.M. Sempere: Exploring regular reversibility in Watson-Crick finite automata, The Thirteenth International Symposium on Artificial Life and Robotics 2008 (AROB ’08), 505-509.

A szétvágó-összeillesztő, vagyis a H-rendszerekkel kapcsolatos eredmények:

[Csuhaj-Varjú et al.] E. Csuhaj-Varjú, R. Freund, L. Kari, Gh. Păun: DNA computing based on splicing: universality results, First Annual Pacific Symposium on Biocomputing 1996, 179-190.

[Head] T. Head: Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviours, Bulletin of Mathematical Biology 49 (1987), 737-759.T.

[Head, Pixton] T. Head, D. Pixton: Splicing and Regularity, Recent Advances in Formal Languages and Applications, Springer, (2006), 119-147.

A beszúró-törlő rendszerekkel kapcsolatos eredmények:

[Kari] L. Kari: Insertion and deletion of words: determinism and reversibility, Mathematical Foundations of Computer Science (MFCS 1992), Lecture Notes in Computer Science (LNCS, Springer) 629 (1992), 315-326.

[Margenstern et al.] M. Margenstern, Gh. Păun, Y. Rogozhin, S. Verlan: Context-free insertion-deletion systems, Theoretical Computer Science 320 (2005), 339-348.

[Verlan] S. Verlan: On minimal context-free insertion-deletion systems. Journal of Automata, Languages and Combinatorics (JALC) 12 (2007), 317-328.

A konstruktív modellekkel kapcsolatban ajánljuk:

[Dediu, Nagy] A.H. Dediu, B. Nagy: Self-assembling tilings of Boolean tree-like circuits modelled by contextual hypergraph grammars, International Workshop on Nonlinear Signal and Image Processing (NSIP2007), 150-153.

[Ogihara, Ray] M. Ogihara, A. Ray: Simulating Boolean circuits on a DNA computer, Algorithmica 25 (1999), 239-250.

[Rothemund] P.W.K. Rothemund: Folding DNA to create nanoscale shapes and patterns, Nature 440/7082 (2006), 297-302.

[Winfree et al.] E. Winfree, X. Yang, N.C. Seeman: Universal computation via self-assembly of DNA: some theory and experiments, DNA based computers II. DIMACS series in discrete mathematics and theoretical computer science 44 AMS (1996), 191-213.

Az élő sejtben végbemenő számítási folyamatokhoz ajánlott irodalom:

[Alhazov et al.] A. Alhazov, I. Petre, V. Rogojin: Solutions to computational problems through gene assembly, Natural Computing 7 (2008), 385-401.

[Ehrenfeucht et al.] A. Ehrenfeucht, T. Harju, I. Petre, D.M. Prescott, G. Rozenberg: Computation in living cells: gene assembly in ciliates, Springer, Berlin, Heidelberg, New York 2004.

[Kari, Landweber] L. Kari, L.F. Landweber: Computational power of gene rearrangement. DNA based computers, V. MIT, AMS (1999), 207-216.

[Prescott et al.] D.M. Prescott, A. Ehrenfeucht, G. Rozenberg: Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates, Journal of Theoretical Biology 222 (2001), 323-330.

Egyéb DNS számításokkal kapcsolatos irodalom:

[Blanchet-Sadri] F. Blanchet-Sadri, Algorithmic combinatorics on partial words, Chapman & Hall/CRC Press, Boca Raton, FL, 2008.

[Cavaliere, Leupold] M. Cavaliere, P. Leupold: Computing by observing: Simple systems and simple observers, Theoretical Computer Science 412 (2011), 113-123.

[Loos, Nagy] R. Loos, B. Nagy: On the concepts of parallelism in biomolecular computing, Triangle: Language, Literature, Computation 6 (2011), 109-118.

[Nagy, Battyányi] B. Nagy, P. Battyányi: DNA-Prolog, Programs, proofs, processes: 6th Conference on Computability in Europe (CIE 2010), Booklet, 281-290.

[Uejima et al.] H. Uejima, M. Hagiya, S. Kobayashi: Horn clause computation by self-assembly of DNA molecules, DNA Computing 2001, Lecture Notes in Computer Science (LNCS, Springer) 2340 (2002), 308-320.

Az (elméleti) számítástudományhoz ajánlott irodalom:

[Dömösi et al.] Dömösi P., Falucskai J., Horváth G., Mecsei Z., Nagy, B.: Formális Nyelvek és Automaták, egyetemi jegyzet (Kelet-magyarországi Informatika Tananyag Tárház), Debrecen, 2011.

[Hopcroft, Ullman] J.E. Hopcroft, J.D. Ullman: Introduction to Automata Theory, Languages, and Computation, Addison-Wesley, Reading, Massachusetts, Menlo Park, California, London, Amsterdam, Don Mills, Ontario, Sidney, 1979.

[Papadimitriou] C.H. Papadimitriou: Számítási bonyolultság, Addison-Wesley, 1995., magyar fordítás: Novadat Bt. 1999.

[Demetrovics et al.] Demetrovics J., J. Denev, R. Pavlov: A számítástudomány matematikai alapjai, Tankönyvkiadó, Budapest, 1989.