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Circular Suggestions for DNA Computing
 Pattern Formation in Biology, Vision and Dynamics: 325335. World Scientific
"... This article arose from a reading of the paper of Q.Ouyang, P.D.Kaplan, S.Liu and A.Libchaber ..."
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This article arose from a reading of the paper of Q.Ouyang, P.D.Kaplan, S.Liu and A.Libchaber
YAC: Yet Another Computation Model of SelfAssembly
, 1999
"... . This paper proposes a new model for DNA computation termed YAC based on selfassembly principle. The model has three advantages: (i) It has the universal computability of Turing machines. (ii) It requires only simple and basic molecular biological operations. Besides annealing and melting in a o ..."
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. This paper proposes a new model for DNA computation termed YAC based on selfassembly principle. The model has three advantages: (i) It has the universal computability of Turing machines. (ii) It requires only simple and basic molecular biological operations. Besides annealing and melting in a onepot reaction, only the detection of a completely hybridized double stranded molecule is used. (iii) Therefore, a molecular biological implementation of the model seems highly feasible. In order to make YAC computation more resource efficient, we introduce an incremental computation method. 1. Introduction In recent intensive study of normal form theorems for the generative grammars in formal language theory, quite a few number of normal form theorems for a variety of types of grammars have been presented, ranging from regular grammars to phrasestructure grammars in Chomsky's hierarchy. Among others, some of the normal forms for phrasestructure grammars can be of crucially importance wh...
On the Universality of Post and Splicing Systems
 Biocomputing: Proceedings of the 1996 Pacific Symposium pages 288299. World Scientific Publishing Co
, 1996
"... In search for a universal splicing system, in this paper we present a Post system universal for the class of Post systems, and we discuss its translation into an extended splicing system with multiplicity. We also discuss the complexity of the resulting universal splicing system, comparing our resul ..."
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In search for a universal splicing system, in this paper we present a Post system universal for the class of Post systems, and we discuss its translation into an extended splicing system with multiplicity. We also discuss the complexity of the resulting universal splicing system, comparing our result with recent known results about the translation of universal Turing machines into splicing systems. 1 Introduction Since the possibility of molecular computing was shown by Adleman's pioneering work ([1]) which, in a test tube, experimentally solves a small instance of an NPcomplete problem, the theoretical formalization of such a new computing technology has been attracting much attention in computer science ([3][5][6][12][17]). One of the formal frameworks for molecular computations is the Tom Head's splicing system ( or H system ), which gives a theoretical foundation for computing based on DNA recombination. Tom Head's seminal work ([9]) on modeling DNA recombination as a splicing sys...
Using DNA to solve the Bounded Post Correspondence Problem
, 2000
"... Introduction Molecular computing, known also under the name of biomolecular computing, biocomputing or DNA computing, is a new computation paradigm that employs (bio)molecule manipulation to solve computational problems. The excitement generated by the first successful experiment (Adleman 1994, [1] ..."
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Introduction Molecular computing, known also under the name of biomolecular computing, biocomputing or DNA computing, is a new computation paradigm that employs (bio)molecule manipulation to solve computational problems. The excitement generated by the first successful experiment (Adleman 1994, [1]) was due to the fact that computing with biomolecules (mainly DNA) offered an entirely new way of performing and looking at computations: the main idea was that data could be encoded in DNA strands, and molecular biology techniques could be used to execute computational operations. Besides the novelty of the approach, molecular computing has the potential to outperform electronic computers. For example, DNA computing has the potential to provide huge memories: DNA in weak solution in one liter of water can encode 10 19 bytes, and one can perform massively parallel associative searches on these memories, [6], [42]. Computing with DNA also has the potential to supply ma
Computation = Selfassembly + Conformational Change: Toward New Computing Paradigms
 Department of Mathematics, School of Education, Waseda University
, 1999
"... . Molecular Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer scie ..."
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. Molecular Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer science (e.g., [2, 3, 7, 9, 10, 11, 13, 17, 19, 20]), trying to break through the socalled NPcompleteness barrier or to establish new computation paradigms with universal capability. This paper proposes new computing paradigms based on selfassembly and conformational change. These two principles have already appeared in an extensive variety of literature in natural science, while relatively a few studies have discussed these two together in the context of computing. In order to demonstrate a new computing schema : computation = selfassembly + conformational change, we first discuss a framework of computing model CCC (Computing by Conformational Change) by showing examples of solving several N...
DNA computing in vitro and in vivo
 In Future generation computer systems, Elsevier Science. In
"... This is a review paper addressing two main aspects of DNA computing research: DNA computing in vitro (in the test tube) and in vivo (in a living organism). We describe the first successful in vitro DNA computing experiment [L.M. Adleman, Science 266 (1994) 1021–1024] which solved a mathematical prob ..."
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This is a review paper addressing two main aspects of DNA computing research: DNA computing in vitro (in the test tube) and in vivo (in a living organism). We describe the first successful in vitro DNA computing experiment [L.M. Adleman, Science 266 (1994) 1021–1024] which solved a mathematical problem, the Directed Hamiltonian Path Problem, solely by manipulation of DNA strands in test tubes. We then address DNA computing in vivo by presenting a model proposed by Head [in: G.
DNA Splicing Systems based on Post Systems
"... . DNA splicing systems (or simply splicing systems) are a new type of generative mechanisms for modeling DNA recombination behaviors, initiated by Tom Head's seminal paper ([8]). For this reason, splicing systems are sometimes called Head systems (H systems), and a number of extensive work on this e ..."
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. DNA splicing systems (or simply splicing systems) are a new type of generative mechanisms for modeling DNA recombination behaviors, initiated by Tom Head's seminal paper ([8]). For this reason, splicing systems are sometimes called Head systems (H systems), and a number of extensive work on this exciting subject have already been reported by many authors. Among others, Paun's recent result shows that extended H systems with finite sets of axioms and regular sets of rules exactly characterize the recursively enumerable languages, thus having the full power of Turing machines ([13]). Also, more recently it is shown that there is a universal extended H system analogous to a universal Turing machine ([4]). This paper concerns further formal study on the generative powers of extended H systems. First, using a classical result by Post which characterizes the recursively enumerable languages in terms of his Post Normal systems, we establish several new characterizations of exten...
Recent Developments in DNAComputing
 IN PROCEEDINGS OF THE 1997 27TH INTERNATIONAL SYMPOSIUM ON MULTIPLEVALUED LOGIC
, 1997
"... In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models was introduced and ..."
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In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models was introduced and examined, concerning their computional power (universality as well as time and space complexity), their efficiency and their error resistance. The main results are presented in this survey.
Computing with Molecules
, 1997
"... In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models have been introduc ..."
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In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models have been introduced, and their computational power has been examined, with results on universality, complexity, efficient algorithms, and error resistance. The main results are presented in this survey.