Abstract not found

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 seven-city 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 ...

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.

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, H-Systems, DNA-computing, biocomputing, bioinformatics, regular languages, finite automata. 1 Introduction The sp...

This paper concerns the formal study on the generative powers of extended splicing

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 NP-Complete, 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...

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 DNA-based 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 Introduction Early models of DNA recombination, the splicing systems, have already been defined by [4]. They aimed to describe the action of restriction enzymes and ligases on DNA molecules which resulted in cleavage and reassociation of DNA strands. Almo...

This article arose from a reading of the paper of Q.Ouyang, P.D.Kaplan, S.Liu and A.Libchaber

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 ground-breaking 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...

Abstract not found