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18
Universal Molecular Computation in Ciliates
 Evolution as Computation
, 2002
"... How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a sevencity Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computin ..."
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Cited by 27 (3 self)
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How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a sevencity Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this "problem", which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. Here we develop a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform at ...
Computational Power of Gene Rearrangement
"... In [8] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model ..."
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Cited by 25 (4 self)
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In [8] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model has the computational power of a Turing machine. This indicates that, in principle, some unicellular organisms may have the capacity to perform any computation carried out by an electronic computer.
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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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...
Formal Language Theory and Biological Macromolecules
 Series in Discrete Mathematics and Theoretical Computer Science
, 1999
"... Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews languagetheoretic approaches to describing intramolecular and intermolecular structural interactions w ..."
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Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews languagetheoretic approaches to describing intramolecular and intermolecular structural interactions within these molecules, and evolutionary relationships between them. 1 Introduction The author has for some time been investigating the application of formal language theory to biological macromolecules, primarily nucleic acids because of the relative simplicity of the biochemical structures and interactions. After introducing the very simple mathematical foundations for these investigations, this article will review three major lines of research. These can largely be found in more fully developed form in referenced publications, though some new material is also included in each case. The sections below will deal with the use of formal grammars to describe intramolecular interactions [17, 18...
Learning Local Languages and Its Application to Protein alphaChain Identification
 PROC. OF 27TH HAWAII INTERNATIONAL CONFERENCE ON SYSTEM SCIENCES
, 1996
"... This paper concerns an efficient algorithm for learning in the limit a special type of regular languages called locally testable languages from positive data, and its application to identifying the protein ffchain region in amino acid sequences. First, we present a linear time algorithm that, give ..."
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Cited by 9 (3 self)
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This paper concerns an efficient algorithm for learning in the limit a special type of regular languages called locally testable languages from positive data, and its application to identifying the protein ffchain region in amino acid sequences. First, we present a linear time algorithm that, given a locally testable language, learns (identifies) its deterministic finite state automaton in the limit from only positive data. This provides us with a practical and efficient learning method for a specific domain of symbolic analysis. We then describe several experimental results using the learning algorithm developed above. Following a theoretical observation which strongly suggests that a certain type of amino acid sequences can be expressed by a locally testable language, we apply the learning algorithm to identifying the protein ffchain region in amino acid sequences for hemoglobin. Experimental scores show an overall success rate of 95 % correct identification for positive data, an...
Reversible Molecular Computation in Ciliates
, 1999
"... We prove that a reversible model for the guided homologous recombinations that take place during gene rearrangement in ciliates has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the c ..."
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Cited by 5 (1 self)
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We prove that a reversible model for the guided homologous recombinations that take place during gene rearrangement in ciliates has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform any computation carried out by an electronic computer.
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
Computing with DNA
 In Computer Methods in Molecular Biology, (S.Misener, S.Krawetz, Eds.), in Methods in Molecular Biology series
, 1998
"... A brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and construction. The means used for performing calculations were whatever was available, and thus progressed gradually from ..."
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A brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and construction. The means used for performing calculations were whatever was available, and thus progressed gradually from manual (digits) to mechanical (abacus, mechanical adding engine), and from there on to electronic devices. Electronic computers are only the latest in a long chain of human efforts to use the best technology available for performing computations. Although it is true that their appearance, some 50 years ago, has revolutionized computing, electronic computers mark neither the beginning nor the end of the history of computation. Indeed, even electronic computers have their limitations: There is a limit to the amount of data they can store, and physical laws dictate the speed thresholds they will soon reach. The most recent attempt to break down these barriers is to replace, once more, the tools for performing computations with biological ones instead of electrical ones. DNA computing (also sometimes referred to as biomolecular computing or molecular computing) is a new computational paradigm that employs (bio)molecule manipulation to solve computational problems, at the same time exploring natural processes as computational models. Research in this area began with an experiment by Leonard Adleman, who surprised the scientific community in 1994 (1) by using the tools of molecular biology to solve a difficult computational problem. Adleman’s experiment solved an instance of the Directed Hamiltonian Path Problem solely by manipulating DNA strands. This marked the first solution of a mathematical problem by use of biology.
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...