Molecular computing paradigm – toward freedom from Turing's charm

This article gives a concise but intensive survey on one of the subfieldsof natural computing – Molecular Computing. Starting with making a brief revisit to Adleman's pioneering work, this paper will give an overviewof selected topics of the field from theory to experiments, while the stressis primarily put on research of theoretical achievements of molecular computing models.

[1]  Ron Weiss,et al.  Engineered Communications for Microbial Robotics , 2000, DNA Computing.

[2]  C. Cantor,et al.  Biophysical chemistry. Part III, The behavior of biologicalmacromolecules , 1980 .

[3]  Takashi Yokomori,et al.  On the Computational Power of Insertion-Deletion Systems , 2002, DNA.

[4]  Joost Engelfriet,et al.  Tree transducers, L systems and two-way machines (Extended Abstract) , 1978, J. Comput. Syst. Sci..

[5]  Gérard Berry,et al.  The chemical abstract machine , 1989, POPL '90.

[6]  Masayuki Yamamoto,et al.  Another Realization of Aqueous Computing with Peptide Nucleic Acid , 2001, DNA.

[7]  Sam M. Kim,et al.  Computational Modeling for Genetic Splicing Systems , 1997, SIAM J. Comput..

[8]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

[9]  Takashi Yokomori,et al.  YAC: Yet another computation model of self-assembly , 1999, DNA Based Computers.

[10]  N. Blackstone Essential Cell Biology: An Introduction to the Molecular Biology of the Cell.Bruce Alberts , Dennis Bray , Alexander Johnson , Julian Lewis , Martin Raff , Keith Roberts , Peter Walter , 1998 .

[11]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[12]  John H. Reif,et al.  DNA-based Cryptography , 1999, Aspects of Molecular Computing.

[13]  E. Winfree Simulations of Computing by Self-Assembly , 1998 .

[14]  Grzegorz Rozenberg,et al.  String Tile Models for DNA Computing by Self-Assembly , 2000, DNA Computing.

[15]  Rani Siromoney,et al.  Circular DNA and Splicing Systems , 1992, ICPIA.

[16]  Susan R. Wilson INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .

[17]  Masami Hagiya,et al.  Towards a system for simulating DNA computing with whiplash PCR , 1999, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406).

[18]  Max H. Garzon,et al.  DNA implementation of nondeterminism , 1997, DNA Based Computers.

[19]  D. Herschlag,et al.  Protein enhancement of hammerhead ribozyme catalysis. , 1993, Science.

[20]  Albert S. Benight,et al.  Thermal denaturation of DNA molecules: A comparison of theory with experiment , 1985 .

[21]  J. Paulauskis,et al.  In Vitro Efficacy of Morpholino-modified Antisense Oligomers Directed against Tumor Necrosis Factor-α mRNA* , 1996, The Journal of Biological Chemistry.

[22]  Michael Conrad Molecular Computing Paradigms - Guest Editor's Introduction , 1992, Computer.

[23]  Giancarlo Mauri,et al.  Parallel Rewriting P Systems with Deadlock , 2002, DNA.

[24]  N Jonoska,et al.  The bounded complexity of DNA computing. , 1999, Bio Systems.

[25]  Masami Hagiya,et al.  From Molecular Computing to Molecular Programming , 2000, DNA Computing.

[26]  Martyn Amos,et al.  DNA simulation of boolean circuits , 1998 .

[27]  P D Kaplan,et al.  DNA solution of the maximal clique problem. , 1997, Science.

[28]  Masami Hagiya,et al.  Improving Sequence Design for DNA Computing , 2000, GECCO.

[29]  G Rozenberg,et al.  Computing with DNA by operating on plasmids. , 2000, Bio Systems.

[30]  B. Alberts,et al.  An Introduction to the Molecular Biology of the Cell , 1998 .

[31]  Peter E. Nielsen,et al.  DNA-like double helix formed by peptide nucleic acid , 1994, Nature.

[32]  Richard M. Karp,et al.  Error-resilient DNA computation , 1999 .

[33]  D. Richman,et al.  Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Douglas Poland,et al.  Theory of helix-coil transitions in biopolymers , 1970 .

[35]  Hiroshi Tanaka,et al.  Artificial Life Applications of a Class of P Systems: Abstract Rewriting Systems on Multisets , 2000, WMP.

[36]  R. Birge Protein-Based Computers , 1995 .

[37]  Erik Winfree,et al.  Universal computation via self-assembly of DNA: Some theory and experiments , 1996, DNA Based Computers.

[38]  T. Head Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. , 1987, Bulletin of mathematical biology.

[39]  Masanori Arita,et al.  Solid phase DNA solution to the Hamiltonian path problem , 1997, DNA Based Computers.

[40]  Gheorghe Păun,et al.  Computing with cells and atoms in a nutshells , 2000 .

[41]  Takashi Yokomori,et al.  Computation = self-assembly + conformational change: toward new computing paradigms , 2000, Developments in Language Theory.

[42]  F Guarnieri,et al.  Maya Blue Paint: An Ancient Nanostructured Material , 1996, Science.

[43]  Rudolf Freund,et al.  Watson-Crick finite automata , 1997, DNA Based Computers.

[44]  Michael Conrad Molecular computing: the lock-key paradigm , 1992, Computer.

[45]  Grzegorz Rozenberg,et al.  Sticker Systems , 1998, Theor. Comput. Sci..

[46]  M Conrad,et al.  DNA as a vehicle for the self-assembly model of computing. , 1998, Bio Systems.

[47]  Claire Mathieu,et al.  Error-resilient DNA computation , 1996, SODA '96.

[48]  Gheorghe Paun,et al.  At the crossroads of DNA computing and formal languages: Characterizing recursively enumerable languages using insertion-deletion systems , 1997, DNA Based Computers.

[49]  Grzegorz Rozenberg,et al.  Handbook of formal languages, vol. 3: beyond words , 1997 .

[50]  J W Szostak,et al.  RNA-peptide fusions for the in vitro selection of peptides and proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Masami Hagiya,et al.  Successive State Transitions with I/O Interface by Molecules , 2000, DNA Computing.

[52]  Yasubumi Sakakibara Solving Computational Learning Problems of Boolean Formulae on DNA Computers , 2000, DNA Computing.

[53]  Chris Hanson,et al.  Amorphous computing , 2000, Commun. ACM.

[54]  Gheorghe Paun,et al.  DNA Computing, Matching Systems, and Universality , 1996 .

[55]  Gheorghe Paun (DNA) computing by carving , 1999, Soft Comput..

[56]  M. Frank-Kamenetskii,et al.  A theoretical analysis of specificity of nucleic acid interactions with oligonucleotides and peptide nucleic acids (PNAs). , 1998, Journal of molecular biology.

[57]  J. McCaskill,et al.  Cooperative amplification of templates by cross-hybridization (CATCH). , 1997, European journal of biochemistry.

[58]  Masanori Arita,et al.  Stepwise Generation of Hamiltonian Path with Molecules , 1997, Biocomputing and Emergent Computation.

[59]  Masami Hagiya,et al.  Virtual DNA simulator and protocol design by GA , 1999 .

[60]  M. Hagiya,et al.  State transitions by molecules. , 1999, Bio Systems.

[61]  Leslie G. Valiant,et al.  Computational limitations on learning from examples , 1988, JACM.

[62]  Gheorghe Paun,et al.  On the Splicing Operation , 1996, Discret. Appl. Math..

[63]  Tony L. Eng Linear DNA self-assembly with hairpins generates linear context-free grammars , 1997, DNA Based Computers.

[64]  Stuart A. Kurtz,et al.  Active transport in biological computing , 1996, DNA Based Computers.

[65]  Rudolf Freund,et al.  DNA Computing Based on Splicing: The Existence of Universal Computers , 1999, Theory of Computing Systems.

[66]  A Suyama,et al.  Intelligent DNA chips: logical operation of gene expression profiles on DNA computers. , 2000, Genome informatics. Workshop on Genome Informatics.

[67]  Tero Harju,et al.  Splicing semigroups of dominoes and DNA , 1991, Discret. Appl. Math..

[68]  Hartmut Ehrig,et al.  Formal and Natural Computing , 2002, Lecture Notes in Computer Science.

[69]  Marilena Barnabei,et al.  Some properties of characteristic polynomials and applications to T-lattices , 1991, Discret. Math..

[70]  Gheorghe Paun,et al.  DNA computing, sticker systems, and universality , 1998, Acta Informatica.

[71]  Satoshi Kobayashi,et al.  DNA-EC: A model of DNA-computing based on equality checking , 1997, DNA Based Computers.

[72]  Erik Winfree,et al.  On the computational power of DNA annealing and ligation , 1995, DNA Based Computers.

[73]  Masami Hagiya,et al.  DNA computation simulator based on abstract bases , 2001, Soft Comput..

[74]  Gheorghe Paun,et al.  Simulation Algorithms for Computational Systems Biology , 2017, Texts in Theoretical Computer Science. An EATCS Series.

[75]  Erik Winfree,et al.  A sticker based model for DNA computation , 1996, DNA Based Computers.

[76]  R. Smullyan Theory of formal systems , 1962 .

[77]  Yasubumi Sakakibara Population Computation and Majority Inference in Test Tube , 2001, DNA.

[78]  W. Stemmer Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[79]  Russell J. Deaton,et al.  The Fidelity of Annealing-Ligation: A Theoretical Analysis , 2000, DNA Computing.

[80]  Erik Winfree,et al.  The program-size complexity of self-assembled squares (extended abstract) , 2000, STOC '00.

[81]  Gheorghe Paun Computing with Bio-Molecules: Theory and Experiments , 1999 .

[82]  Arto Salomaa,et al.  Computation and Automata , 1984 .

[83]  Eric B. Baum,et al.  DNA sequences useful for computation , 1996, DNA Based Computers.

[84]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[85]  Gheorghe Paun,et al.  Regular Extended H Systems are Computationally Universal , 1996, J. Autom. Lang. Comb..

[86]  Richard J. Lipton,et al.  Making DNA computers error resistant , 1996, DNA Based Computers.

[87]  James G. Wetmur Physical chemistry of nucleic acid hybridization , 1997, DNA Based Computers.

[88]  Amit Marathe,et al.  On combinatorial DNA word design , 1999, DNA Based Computers.

[89]  T. Head,et al.  Aqueous computing: writing on molecules , 1999, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406).

[90]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[91]  Gheorghe Paun,et al.  DNA Computing: New Computing Paradigms , 1998 .

[92]  Leonard M. Adleman,et al.  On constructing a molecular computer , 1995, DNA Based Computers.

[93]  Michael Conrad,et al.  On design principles for a molecular computer , 1985, CACM.

[94]  W. W. Peterson,et al.  Error-Correcting Codes. , 1962 .

[95]  Liberman Ea,et al.  [Letter: Molecular computer. II. Formal description (system of operators)]. , 1973 .

[96]  H. B. Mann Error-Correcting Codes , 1972 .

[97]  Tom Head CIRCULAR SUGGESTIONS FOR DNA COMPUTING , 2000 .

[98]  Satoshi Kobayashi,et al.  Multiple splicing systems and the universal computability , 2001, Theor. Comput. Sci..

[99]  Bruce Alberts,et al.  Essential Cell Biology , 1983 .

[100]  N. Jonoska,et al.  Three dimensional DNA structures in computing. , 1999, Bio Systems.

[101]  Aviezri S. Fraenkel Protein folding, spin glass and computational complexity , 1997, DNA Based Computers.

[102]  Lila Kari,et al.  DNA Computers: Tomorrow's Reality , 2001, Current Trends in Theoretical Computer Science.

[103]  Cristian S. Calude,et al.  Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing , 2000 .

[104]  Gheorghe Paun,et al.  Computing with Membranes , 2000, J. Comput. Syst. Sci..

[105]  R R Breaker,et al.  Emergence of a replicating species from an in vitro RNA evolution reaction. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[106]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[107]  Emil L. Post Formal Reductions of the General Combinatorial Decision Problem , 1943 .

[108]  Michael S. Waterman,et al.  Introduction to computational biology , 1995 .

[109]  Masami Hagiya,et al.  Joining and rotating data with molecules , 1997, Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97).

[110]  D. Pixton Linear and circular splicing systems , 1995, Proceedings First International Symposium on Intelligence in Neural and Biological Systems. INBS'95.

[111]  Erzsébet Csuhaj-Varjú,et al.  Test Tube Distributed Systems Based on Splicing , 1996, Comput. Artif. Intell..

[112]  Jules Moreau,et al.  Molecular Computation by DNA Hairpin Formation , 2000 .

[113]  Yasubumi Sakakibara,et al.  Splicing on tree-like structures , 1997, DNA Based Computers.

[114]  Takashi Yokomori,et al.  DNA implementation of simple Horn clause computation , 1997, Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97).

[115]  Hiroshi Yoshida,et al.  Solution to 3-SAT by breadth first search , 1999, DNA Based Computers.

[116]  F. C. Hennie,et al.  One-Tape, Off-Line Turing Machine Computations , 1965, Inf. Control..

[117]  Viliam Geffert Normal forms for phrase-structure grammars , 1991, RAIRO Theor. Informatics Appl..

[118]  Gheorghe Paun,et al.  Language Theory and Molecular Genetics: Generative Mechanisms Suggested by DNA Recombination , 1997, Handbook of Formal Languages.

[119]  Cristian S. Calude,et al.  Proceedings of the Workshop on Multiset Processing: Multiset Processing, Mathematical, Computer Science, and Molecular Computing Points of View , 2000 .

[120]  J Reif,et al.  Micro flow bio-molecular computation. , 1999, Bio Systems.

[121]  Satoshi Kobayashi,et al.  On the power of circular splicing systems and DNA computability , 1997, Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97).

[122]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[123]  Richard J. Lipton,et al.  On the Computational Power of DNA , 1996, Discret. Appl. Math..

[124]  Gheorghe Paun,et al.  Regulated Rewriting in Formal Language Theory , 1989 .

[125]  Masami Hagiya,et al.  Towards parallel evaluation and learning of Boolean μ-formulas with molecules , 1997, DNA Based Computers.

[126]  Satoshi Kobayashi,et al.  Horn Clause Computation with DNA Molecules , 1999, J. Comb. Optim..

[127]  Lloyd M. Smith,et al.  DNA computing on surfaces , 2000, Nature.

[128]  Elizabeth Laun,et al.  Wet splicing systems , 1997, DNA Based Computers.

[129]  Richard J. Lipton,et al.  DNA Based Computers , 1996 .

[130]  Y Husimi,et al.  In vitro virus: Bonding of mRNA bearing puromycin at the 3′‐terminal end to the C‐terminal end of its encoded protein on the ribosome in vitro , 1997, FEBS letters.

[131]  K Saitou Self-assembling automata: a model of conformational self-assembly. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[132]  Chew Lim Tan,et al.  Knowledge-Based Simulation of Regulatory Action in lambda phage , 1995, Int. J. Artif. Intell. Tools.

[133]  Grzegorz Rozenberg,et al.  DNA Computing: New Ideas and Paradigms , 1999, ICALP.

[134]  John H. Reif,et al.  Parallel molecular computation , 1995, SPAA '95.

[135]  Mitsunori Ogihara,et al.  DNA-Based Self-Propagating Algorithm for Solving Bounded-Fan-In Boolean Circuits , 1999 .

[136]  Kazuhiro Saitou,et al.  On Classes of One-dimensional Self-assembling Automata , 1996, Complex Syst..

[137]  Grzegorz Rozenberg,et al.  Handbook of Formal Languages , 1997, Springer Berlin Heidelberg.

[138]  Erik Winfree,et al.  Experimental progress in computation by self-assembly of DNA tilings , 1999, DNA Based Computers.

[139]  Satoshi Kobayashi,et al.  Sticker systems with complex structures , 2001, Soft Comput..

[140]  John H. Reif,et al.  Paradigms for Biomolecular Computation , 1998 .

[141]  Satoshi Kobayashi,et al.  A Magic Pot : Self-assembly Computation Revisited , 2002, Formal and Natural Computing.

[142]  Max H. Garzon,et al.  Good encodings for DNA-based solutions to combinatorial problems , 1996, DNA Based Computers.

[143]  L F Landweber,et al.  Computing with DNA. , 2000, Methods in molecular biology.

[144]  Michail G. Lagoudakis,et al.  2D DNA self-assembly for satisfiability , 1999, DNA Based Computers.