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On the Power of Circular Splicing Systems and DNA Computability
 Proc. of IEEE Intern. Conf. on Evol. Comput. (ICEC'97
, 1997
"... From a biological motivation of interactions between linear and circular DNA sequences, we propose a new type of splicing models called circular H systems and show that they have the same computational power as Turing machines. It is also shown that there effectively exists a universal circular H sy ..."
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From a biological motivation of interactions between linear and circular DNA sequences, we propose a new type of splicing models called circular H systems and show that they have the same computational power as Turing machines. It is also shown that there effectively exists a universal circular H system which can simulate any circular H system with the same terminal alphabet, which strongly suggests a feasible design for a DNA computer based on circular splicing. 1 Introduction Since Adleman's breathtaking paper on molecular (DNA) computing ([1]), there have already been quite a few papers on this challenging topic : [10] shows how to solve NPcomplete problems using DNA, while [3] discusses a design method for simulating a Turing machine by molecular biological techniques and shows how to compute PSPACE, and [4]) gives a methodology for breaking the DES using techniques in genetic engineering. In response to the rapid stream of experimental research on this new computation paradigm...
DNA Computing Based on Splicing: Universality Results
, 1997
"... First, we recall some characterizations of recursively enumerable languages by means of finite H systems with certain regulations on the splicing operation. Then, we consider a variant of the splicing operation where the splicing proceeds always in couples of steps: the two strings obtained after a ..."
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Cited by 10 (0 self)
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First, we recall some characterizations of recursively enumerable languages by means of finite H systems with certain regulations on the splicing operation. Then, we consider a variant of the splicing operation where the splicing proceeds always in couples of steps: the two strings obtained after a splicing enter immediately a second splicing (the rules used in the two steps are not prescribed). Somewhat surprising if we take into account the loose control on the performed operations, extended H systems with finite sets of axioms and of splicing rules, using this double splicing operation, can again characterize the recursively enumerable languages. Finally, we consider twotypes of distributed H systems: communicating distributed H systems and timevarying distributed H systems. For the first type of devices, we give a new proof of the recent result of [24] that (in the extended case) such systems with three components characterize the recursively enumerable languages. In what...
DNA Computing: Models and Implementations
, 2002
"... As the fabrication of integrated circuits continues to take place on increasingly smaller scales, we grow closer to several fundamental limitations on electronic computers. For many classes of problems, computing devices based on biochemical reactions present an attractive alternative to conventiona ..."
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As the fabrication of integrated circuits continues to take place on increasingly smaller scales, we grow closer to several fundamental limitations on electronic computers. For many classes of problems, computing devices based on biochemical reactions present an attractive alternative to conventional computing paradigms. We present here a survey of the theory and implementation of biologically and biochemically based computers.
Thermodynamic Constraints on DNAbased Computing
 IN GHEORGHE PĂUN, EDITOR, COMPUTING WITH BIOMOLECULES
, 1998
"... Computing with biological macromolecules, such as DNA, is fundamentally a physical/chemical process. The DNA chemistry introduces a level of complexity that makes reliable, efficient, and scalable computations a challenge. All the chemical and thermodynamic factors have to be analyzed and controlled ..."
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Computing with biological macromolecules, such as DNA, is fundamentally a physical/chemical process. The DNA chemistry introduces a level of complexity that makes reliable, efficient, and scalable computations a challenge. All the chemical and thermodynamic factors have to be analyzed and controlled in order for the molecular algorithm to produce the intended result. For instance, a computation based on DNA requires that the problem instance be encoded in single strands of DNA and that these strands react as planned, that molecular biology protocols, such as PCR or affinity separation, correctly extract the result, and that sufficient flexibility remains so that worthwhile computations can be done. In this paper, various thermodynamic and chemical constraints on DNA computing are enumerated. A similarity measure, based on Gibb's free energy of formation, is defined to judge the goodness of DNA encodings. Finally, the DNA computation problem for implementing molecular algorithms is defined, and it is likely that it is as difficult as the combinatorial optimization problems they are intended to solve.
Arithmetically Controlled H Systems
 PRENTICEHALL, ISBN
, 2000
"... We consider two classes of restricted H systems, both dealing with numbers associated to the terms of splicing operations. In one of them, these numbers indicate the age of the strings (the generation when the strings are produced), in the second one the numbers can be interpreted as valences of th ..."
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We consider two classes of restricted H systems, both dealing with numbers associated to the terms of splicing operations. In one of them, these numbers indicate the age of the strings (the generation when the strings are produced), in the second one the numbers can be interpreted as valences of the strings. Restricting the splicing to strings of "a similar age", or accepting as complete splicing processes only those processes which produce strings with a null valence increase the generative power of H systems (with finite sets of rules).
Splicing on Treelike Structures
 Proc. of 3rd DIMACS Workshop on DNA based computers
, 1997
"... In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar notion and a natural extension of splicing systems on strings. Trees are a common and useful data struc ..."
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In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar notion and a natural extension of splicing systems on strings. Trees are a common and useful data structure in computer science and have a biological counterpart such as molecular sequences with secondary structures, which are typical structures in RNA sequences. Splicing on trees involves (1) complete subtrees as axioms, (2) restriction operated on the annealed subsequences, (3) rules to substitute a complete subtree with another. We show that splicing systems on trees with finite sets of axioms and finite sets of rules can generate the class of contextfree languages without the need of multiplicity constraints. 1 Introduction We extend the notion of splicing systems, usually defined on strings, to splicing systems on trees. Splicing systems (also called H systems) have been developed as a...
Separating Some Splicing Models
"... This work shows that the family of languages generated by splicing as defined in the early paper by T. Head is strictly included in the family defined by later de nitions by Head, Gh. Paun, and others. It also proves the strict inclusion of this latter family in the splicing family defined by D. Pix ..."
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This work shows that the family of languages generated by splicing as defined in the early paper by T. Head is strictly included in the family defined by later de nitions by Head, Gh. Paun, and others. It also proves the strict inclusion of this latter family in the splicing family defined by D. Pixton when proving the regularity of splicing languages. We describe instance languages in the difference sets, and prove how they cannot be generated by the smaller families.
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...