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2016 | OriginalPaper | Chapter

16. Biomolecular Computing

Authors : Ke-Lin Du, M. N. S. Swamy

Published in: Search and Optimization by Metaheuristics

Publisher: Springer International Publishing

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Abstract

Biomolecular computing studies the potential of using biological molecules to perform computation. DNA (deoxyribonucleic acid) computing [49] and membrane computing [46] are two natural computing techniques at the biomolecular level. This chapter gives a conceptual introduction to these computing paradigms.

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Literature
1.
Adleman LM. Molecular computation of solutions to combinatorial problems. Science. 1994;266(5187):1021–4.CrossRef
2.
Albert R, Othmer HG. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol. 2003;223(1):1–18.MathSciNetCrossRef
3.
Alhazov A, Martin-Vide C, Pan L. Solving a PSPACE complete problem by recognizing P systems with restricted active membranes. Fundamenta Informaticae. 2003;58(2):67–77.MathSciNetMATH
4.
Baum EB. Building an associative memory vastly larger than the brain. Science. 1995;268:583–5.CrossRef
5.
Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E. Programmable and autonomous computing machine made of biomolecules. Nature. 2001;414:430–4.CrossRef
6.
Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature. 2004;429(6990):423–9.CrossRef
7.
8.
Calude CS, Paun G. Bio-steps beyond Turing. BioSystems. 2004;77:175–94.
9.
Cecilia JM, Garcia JM, Guerrero GD, Martinez-del-Amor MA, Perez-Hurtado I, Perez-Jimenez MJ. Simulation of P systems with active membranes on CUDA. Briefings Bioinform. 2010;11(3):313–22.CrossRef
10.
Chen H, Anindya D, Goel A. Towards programmable molecular machines. In: Proceedings of the 5th conference on foundation of nanoscience, Snowbird, Utah, 2008. p. 137–139.
11.
12.
Chen H, Ionescu M, Ishdorj T. On the efficiency of spiking neural P systems. In: Gutierrez-Naranjo MA, Paun G, Riscos-Nunez A, Romero-Campero FJ, editors. Proceedings of fourth brainstorming week on membrane computing, Sevilla, Spain, February 2006. p. 195–206.
13.
Cheng J, Zhang G, Zeng X. A novel membrane algorithm based on differential evolution for numerical optimization. Int J Unconv Comput. 2011;7:159–83.
14.
Clelland CT, Risca V, Bancroft C. Hiding messages in DNA microdots. Nature. 1999;399(6736):533–4.CrossRef
15.
Cox JP. Long-term data storage in DNA. Trends Biotechnol. 2001;19(7):247–50.CrossRef
16.
Diaz-Pernil D, Gutierrez-Naranjo MA, Perez-Jimenez MJ, Riscos-Nuez A. A linear-time tissue P system based solution for the 3-coloring problem. Electron Notes Theor Comput Sci. 2007;171(2):81–93.
17.
Dittrich P, Ziegler J, Banzhaf W. Artificial chemistries—a review. Artif Life. 2001;7(3):225–75.
18.
Faulhammer D, Cukras AR, Lipton RJ, Landweber LF. Molecular computation: RNA solutions to chess problems. Proc Nat Acad Sci U.S.A. 2000;97:1385–9.CrossRef
19.
Fisher MJ, Paton RC, Matsuno K. Intracellular signalling proteins as ‘smart’ agents in parallel distributed processes. BioSystems. 1999;50(3):159–71.CrossRef
20.
Frisco P. Computing with cells: advances in membrane computing. Oxford: Oxford University Press; 2009.CrossRefMATH
21.
Frisco P. P Systems and unique-sum sets. In: Proceedings of international conference on membrane computing, Lecture notes of computer science 6501. Berlin: Springer; 2010. p. 208–225.
22.
Garcia-Arnau M, Perez D, Rodriguez-Paton A, Sosik P. On the power of elementary features in spiking neural P systems. Nat Comput. 2008;7:471–83.MathSciNetCrossRefMATH
23.
Gheorghe M, Stannett M. Membrane system models for super-Turing paradigms. Nat Comput. 2012;11:253–9.
24.
Grumbach S, Tahi F. A new challenge for compression algorithms: genetic sequences. Inf Process Manag. 1994;30:875–86.CrossRefMATH
25.
Grumbach S, Tahi F. Compression of DNA sequences. In: Proceedings of data compression conference, Snowbird, UT, March 1993. p. 340–350.
26.
Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 2002;420:224–30.CrossRef
27.
Heider D, Barnekow A. DNA-based watermarks using the DNA-crypt algorithm. BMC Bioinform. 2007;8:176.CrossRef
28.
29.
Ionescu M, Paun G, Yokomori T. Spiking neural P systems. Fundamenta Informaticae. 2006;71:279–308.
30.
Ionescu M, Paun G, Yokomori T. Spiking neural P systems with an exhaustive use of rules. Int J Unconv Comput. 2007;3(2):135–53.
31.
Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol. 2004;22:841–7.CrossRef
32.
Ishdorj T, Leporati A, Pan L, Zeng X, Zhang X. Deterministic solutions to QSAT and Q3SAT by spiking neural P systems with pre-computed resources. Theor Comput Sci. 2010;411:2345–58.MathSciNetCrossRefMATH
33.
Kan A, Sakai Y, Shohda K, Suyama A. A DNA based molecular logic gate capable of a variety of logical operations. Nat Comput. 2014;13:573–81.MathSciNetCrossRefMATH
34.
Karakose M, Cigdem U. QPSO-based adaptive DNA computing algorithm. Sci World J. 2013;2013:8. Article ID 160687.
35.
Lauffenburger DA. Cell signaling pathways as control modules: complexity for simplicity? PNAS. 2000;97(10):5031–3.CrossRef
36.
Leporati A, Besozzi D, Cazzaniga P, Pescini D, Ferretti C. Computing with energy and chemical reactions. Nat Comput. 2010;9:493–512.MathSciNetCrossRefMATH
37.
Lin L, Guo F, Xie X. Novel informative feature samples extraction model using cell nuclear pore optimization. Eng Appl Artif Intell. 2015;39:168–80.CrossRef
38.
Maass W. Computing with spikes. Found Inf Process TELEMATIK. 2002;8:32–6.
39.
Manca V, Bianco L, Fontana F. Evolution and oscillation in P systems: applications to biological phenomena. In: Mauri G, Paun G, Perez-Jimenez MJ, Rozenberg G, Salomaa A, editors. Workshop on membrane computing, Lecture notes in computer science 3365. Berlin: Springer; 2004. p. 63–84.
40.
Marijuan PC. Enzymes, artificial cells and the nature of biological information. BioSystems. 1995;35:167–70.CrossRef
41.
Martin-Vide C, Paun G, Pazos J, Rodriguez-Paton A. Tissue P systems. Theor Comput Sci. 2003;296(2):295–326.
42.
43.
Nguyen V, Kearney D, Gioiosa G. An implementation of membrane computing using reconfigurable hardware. Comput Inform. 2008;27:551–69.MathSciNet
44.
45.
46.
47.
48.
Paun G, Rozenberg G, Salomaa A, editors. Handbook of membrane computing. Oxford, UK: Oxford University Press; 2010.MATH
49.
50.
Peng H, Luo X, Gao Z, Wang J, Pei Z. A novel clustering algorithm inspired by membrane computing. Sci World J. 2015;2015:8. Article ID 929471.
51.
Perez-Jimenez MJ, Romero-Jimenez A, Sancho-Caparrini F. Complexity classes in models of cellular computing with membranes. Nat Comput. 2003;2(3):265–85.MathSciNetCrossRefMATH
52.
53.
Qian L, Winfree E. A simple DNA gate motif for synthesizing large-scale circuits. In: DNA computing, Volume 5347 of Lecture notes in computer science. Berlin: Springer; 2008. p. 70–89.
54.
Rothemund P. A DNA and restriction enzyme implementation of turing machines. In: DNA based computers, DIMACS series in discrete mathematics and theoretical computer science, no. 27. Providence, RI: American Mathematical Society; 1996. p. 75–120.
55.
Seelig G, Soloveichik D, Zhang DY, Winfree E. Enzyme-free nucleic acid logic circuits. Science. 2006;314(5805):1585.CrossRef
56.
57.
Stojanovic MN, Mitchell TE, Stefanovic D. Deoxyribozyme-based logic gates. J Am Chem Soc. 2002;124(14):3555–61.CrossRef
58.
59.
Weiss R, Basu S, Hooshansi S, Kalmbach A, Karig D, Mehreja R, Netravalt I. Genetic circuit building blocks for cellular computation, communications, and signal processing. Nat Comput. 2003;2:47–84.CrossRef
60.
Weiss R, Knight Jr TF, Sussman G. Genetic process engineering. In: Amos M, editor. Cellular computation. Oxford, UK: Oxford University Press; 2004. p. 43–73.
61.
Win MN, Smolke CD. Higher-order cellular information processing with synthetic RNA devices. Science. 2008;322(5900):456–60.CrossRef
62.
Wong PC, Wong K, Foote H. Organic data memory using the DNA approach. Commun ACM. 2003;46(1):95–8.CrossRef
63.
Xu J, Qiang X, Yang Y, Wang B, Yang D, Luo L, Pan L, Wang S. An unenumerative DNA computing model for vertex coloring problem. IEEE Trans Nanobiosci. 2011;10(2):94–8.CrossRef
64.
65.
Yurke B, Turberfield A, Mills A Jr, Simmel F, Neumann J. A DNA-fuelled molecular machine made of DNA. Nature. 2000;406:605–8.CrossRef
66.
Zandron C, Ferretti C, Mauri G. Solving NP-complete problems using P systems with active membranes. In: Antoniou CS, Calude MJ, Dinneen I, editors. Unconventional models of computation. London: Springer; 2000. p. 289–301.
67.
Zhang GX, Gheorghe M, Wu CZ. A quantum-inspired evolutionary algorithm based on P systems for knapsack problem. Fundamenta Informaticae. 2008;87:93–116.MathSciNetMATH
Metadata
Title
Biomolecular Computing
Authors
Ke-Lin Du
M. N. S. Swamy
Copyright Year
2016
Book
Search and Optimization by Metaheuristics

Print ISBN: 978-3-319-41191-0

Electronic ISBN: 978-3-319-41192-7

Copyright Year: 2016

DOI
https://doi.org/10.1007/978-3-319-41192-7_16

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