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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 ..."
Abstract

Cited by 22 (5 self)
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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...
Splicing representations of strictly locally testable languages
 Discrete Appl. Math
, 1998
"... ..."
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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Cited by 2 (0 self)
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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...
DNA computing based on insertions and deletions
"... is the simple observation that the following two processes, one biological and one mathematical, are analogous: (a) the very complex structure of a living being is the result of applying simple operations (copying, splicing, etc.) to initial information encoded in a DNA sequence, (b) the result f(w) ..."
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is the simple observation that the following two processes, one biological and one mathematical, are analogous: (a) the very complex structure of a living being is the result of applying simple operations (copying, splicing, etc.) to initial information encoded in a DNA sequence, (b) the result f(w) of applying a computable function to an argument w can be obtained by applying a combination of basic simple functions to w (see Section?? or [42] for details). If noticing this analogy were the only ingredient necessary to cook a computing DNA soup, we would have been playing computer games on our DNA laptops a long time ago! It took in fact the ripening of several factors and a renaissance mind like Adleman’s, a mathematician knowledgeable in biology, to bring together these apparently independent phenomena. Adleman realized that not only are the two processes similar but, thanks to the advances in molecular biology technology, one can use the biological to simulate the mathematical.
DNA Computing and Molecular SelfAssembly Area Exam
"... problem by encoding it in DNA and subsequently using a biological protocol that can create and extract the solution in a small number of steps. The main attraction of this method of performing computation lies in the potential of massive parallelism resulting in a greater number of computations per ..."
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problem by encoding it in DNA and subsequently using a biological protocol that can create and extract the solution in a small number of steps. The main attraction of this method of performing computation lies in the potential of massive parallelism resulting in a greater number of computations per second than the fastest supercomputers could perform (Adleman, 1994, Gifford, 1994). Other motivations include the informationencoding density of DNA that exceeds that of conventional computers, and the energy efficiency of enzymes, that could result in very low energy computations (Adleman, 1994, Gifford, 1994). The idea of using DNA to perform computations is earlier than this work, as it appeared in the splicing systems of Head (1987, 1992) that propose the use of onedimensional selfassembly of doublestranded DNA together with enzymes capable of cutting DNA at sites that contain specific patterns. Below we discuss the main ideas in the method of Adleman (1994), and in some of the related work that emerged. We will try to briefly cover the main issues involved in using this work to perform practical computations. We assume that the reader is familiar with the basic structure of single and doublestranded DNA molecules, their basic properties such as annealing of complementary strands, and basic biological assays such as Polymerase Chain Reaction (PCR),