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22
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 computing, which in a few years h ..."
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Cited by 21 (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 20 (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.
Dna Splicing Systems And Post Systems
, 1996
"... This paper concerns the formal study on the generative powers of extended splicing ..."
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Cited by 8 (2 self)
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This paper concerns the formal study on the generative powers of extended splicing
DNA Implementation of Simple Horn Clause Computation
, 1997
"... In this paper, we propose a method for biologically implementing simple Boolean formulae. This method enables us to compute logical consequences of a given set of simple Horn clauses in parallel and takes advantage of potentially huge number of molecular CPUs of DNA computers. Further, we show that ..."
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Cited by 7 (0 self)
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In this paper, we propose a method for biologically implementing simple Boolean formulae. This method enables us to compute logical consequences of a given set of simple Horn clauses in parallel and takes advantage of potentially huge number of molecular CPUs of DNA computers. Further, we show that the method is nicely applied to the parallel implementation of a grammatical recognition algorithm which is based on `dynamic programming. ' 1 Introduction Adleman's work on the DNA implementation of computing a given instance of directed Hamiltonian path problem, which is known to be NPComplete, opens the door to the highly parallel computation using `molecules'([Adl94]). His study was followed by many researches: generalizing his technique([Lip95a][Lip95b]), providing abstract DNA computer models with Turing computability([Adl95] [Bea95][WR95]), and so forth. In spite of those efforts on pursuing possible implementation of DNA computers with Turing computability using a finite set of bio...
Circular contextual insertions/deletions with applications to biomolecular computation
 In: Proc. of 6th Int. Symp. on String Processing and Information Retrieval, SPIRE’99 (Cancun
, 1999
"... Insertions and deletions of small circular DNA strands into long linear DNA strands are phenomena that happen frequently in nature and thus constitute an attractive paradigm for biomolecular computing. This paper presents a new model for DNAbased computation that involves circular as well as linear ..."
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Cited by 7 (0 self)
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Insertions and deletions of small circular DNA strands into long linear DNA strands are phenomena that happen frequently in nature and thus constitute an attractive paradigm for biomolecular computing. This paper presents a new model for DNAbased computation that involves circular as well as linear molecules, and that uses the operations of insertion and deletion. After introducing the formal model we investigate its properties and prove in particular that the circular insertion/deletion systems are capable of universal computation. We also give the results of an experimental laboratory implementation of our model. This shows that rewriting systems of the circular insertion/deletion type are viable alternatives in DNA computation. 1
Splicing Languages Generated with One Sided Context
 Computing With Biomolecules{Theory and Experiments
, 1997
"... The splicing system concept was created in 1987 to allow the convenient representation in formal language theoretic terms of recombinant actions of certain sets of enzymes on double stranded DNA molecules. Characterizations are given here for those regular languages that are generated by splicing ..."
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Cited by 7 (1 self)
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The splicing system concept was created in 1987 to allow the convenient representation in formal language theoretic terms of recombinant actions of certain sets of enzymes on double stranded DNA molecules. Characterizations are given here for those regular languages that are generated by splicing systems having splicing rules that test context on only one side. An algorithm is given for deciding whether any arbitrary regular language can be generated by a splicing system in which all splicing rules test context on the same side. Schutzenberger's concept of a constant relative to a language provides the tool for constructing the required splicing rules. To provide a potential biochemical example, the formal generative capacity of the restriction enzyme BpmI in the company of a ligase is discussed. Experimental investigation is invited. Key words: Splicing systems, HSystems, DNAcomputing, biocomputing, bioinformatics, regular languages, finite automata. 1 Introduction The sp...
DNAEC: A Model of DNAComputing Based on Equality Checking
 Checking, 3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns
, 1997
"... This paper proposes new models for DNA computation based on a simple principle called equality checking. The advantages of the proposed models may include (i) the universal computability of the general models, (ii) the clarity and simplicity of molecular biological operations employed, and therefor ..."
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Cited by 5 (0 self)
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This paper proposes new models for DNA computation based on a simple principle called equality checking. The advantages of the proposed models may include (i) the universal computability of the general models, (ii) the clarity and simplicity of molecular biological operations employed, and therefore (iii) the high feasibility in molecular biological implementation of the models. 1 Introduction Since Adleman's groundbreaking work on the DNA implementation of computing a small instance of directed Hamiltonian path problem ([Adl94]), a numerous number of research papers on this new computation paradigm have been published. In fact, Adleman's model has been extensively studied by many researches, for generalizing his technique to solve larger class of problems ([Lip95a], [Lip95b],[Bea95]), for providing abstract DNA computer models with Turing computability ([Adl95],[Bea95], [Rot95],[WYS96]), and so forth. In spite of those efforts on pursuing possible implementation methods for DNA com...
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.
From MicroSoft to BioSoft: computing with DNA
 Proc. BCEC’97 (BioComputing and Emergent Computation) Skovde, Sweden, World Scienti c
"... “Jump at the sun and you might at least catch hold of the moon” (Jamaican proverb) 1 From Digits and Beads to Bits and Biomolecules The notion of computing seems nowadays to be so synonymous with computers, that we often seem to forget that electronic computers are relatively new players on the worl ..."
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Cited by 4 (0 self)
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“Jump at the sun and you might at least catch hold of the moon” (Jamaican proverb) 1 From Digits and Beads to Bits and Biomolecules The notion of computing seems nowadays to be so synonymous with computers, that we often seem to forget that electronic computers are relatively new players on the world stage, [31]. Indeed, 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 constructions. The means used for performing calculations were whatever was available, and thus gradually progressed from manual to mechanical, and from there on to electrical devices. Indeed, man started off by counting on his digits, a fact attested by the use of the word digit to mean both “any of the ten numbers from 0 to 9 ” and “a finger, thumb or toe ” (Oxford Advanced Learner’s Dictionary). The need for counting and tracking occurrences in the physical world is witnessed by primitive calendars like the one at Stonehenge, 2,800 B.C., or by primitive calculators like the abacus. The abacus, the most common of which comes from China, was man’s first attempt at automating the counting process, and it involved the idea of positional representation: the value assigned to each bead (pebble, shell) was determined not by its shape but by its position. The transition to a qualitatively superior way of doing computation had to wait until the 17th century when Pascal built the first mechanical adding machine (1642), based on a gear system. In his machine, based on the design of Hero of Alexandria (2 A.D.), a wheel engaged its single tooth with a tenteeth ∗ This paper was written during my visit in Japan supported by the “Research for the