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Contextual Insertions/deletions and Computability
 Information and Computation
, 1996
"... We investigate two generalizations of insertion and deletion of words, that have recently become of interest in the context of molecular computing. Given a pair of words (x; y) called a context, the (x; y)contextual insertion of a word v into a word u is performed as follows. For each occurrence o ..."
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We investigate two generalizations of insertion and deletion of words, that have recently become of interest in the context of molecular computing. Given a pair of words (x; y) called a context, the (x; y)contextual insertion of a word v into a word u is performed as follows. For each occurrence of xy as a subword in u, we include in the result of the contextual insertion the words obtained by inserting v into u, between x and y. The (x; y)contextual deletion operation is defined in a similar way. We study closure properties of the Chomsky families under the defined operations, contextual insclosed and delclosed languages and decidability of existence of solutions to equations involving these operations. Moreover, we prove that every Turing machine can be simulated by a system based entirely on contextual insertions and deletions. 1 Introduction Besides being fundamental in formal language theory, the operations of insertion and deletion have recently become of interest in conne...
Akyildiz, A new nanonetwork architecture using flagellated bacteria and catalytic nanomotors
 Journal of Selected Topics in Communications (JSAC
, 2010
"... Abstract—Molecular communication has been recently proposed for interconnected nanoscale devices as an alternative to classical communication paradigms such as electromagnetic waves, acoustic or optical communication. In this novel approach, the information is encoded as molecules that are transpor ..."
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Abstract—Molecular communication has been recently proposed for interconnected nanoscale devices as an alternative to classical communication paradigms such as electromagnetic waves, acoustic or optical communication. In this novel approach, the information is encoded as molecules that are transported between nanoscale devices within different distances. For short distances (nmmm ranges) there exist molecular motors and calcium signaling techniques to realize the communication. For long distances (mmm ranges), pheromones are used to transport information. In this work, the mediumrange is explored to cover distances from µm to mm and a molecular network architecture is proposed to realize the communication between nanomachines that can be deployed over different (short, medium and long) distances. In addition, two new communication techniques, flagellated bacteria and catalytic nanomotors, are proposed to cover the mediumrange. Both techniques are based on the transport of DNA encoded information between emitters and receivers by means of a physical carrier. Finally, a qualitative comparison of both communication techniques is carried out and some future research topics are pointed out.
A universal functional approach to DNA computing and its experimental practicability
 Proceedings 6th DIMACS Workshop on DNA Based Computers, held at the University of Leiden, Leiden, The Netherlands, 13  17
, 2000
"... . The rapid developments in the field of DNA computing reflects two substantial questions: 1. Which models for DNA based computation are really universal? 2. Which model fulfills the requirements to a universal labpracticable programmable DNA computer that is based on one of these models? This pape ..."
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. The rapid developments in the field of DNA computing reflects two substantial questions: 1. Which models for DNA based computation are really universal? 2. Which model fulfills the requirements to a universal labpracticable programmable DNA computer that is based on one of these models? This paper introduces the functional model DNAHaskell focussing its labpracticability. This aim could be reached by specifying the DNA based operations in accordiance to an analysis of molecular biological processes. The specification is determined by an abstraction level that includes nucleotides and strand end labels like 5'phosphate. Our model is able to describe DNA algorithms for any NPcomplete problem  here exemplified by the knapsack problem  as well as it is able to simulate some established mathematical models for computation. We point out the splicing operation as an example. The computational completeness of DNAHaskell can be supposed. This paper is based on discussions about the ...
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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“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
Using DNA to solve the Bounded Post Correspondence Problem
, 2000
"... Introduction Molecular computing, known also under the name of biomolecular computing, biocomputing or DNA computing, is a new computation paradigm that employs (bio)molecule manipulation to solve computational problems. The excitement generated by the first successful experiment (Adleman 1994, [1] ..."
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Introduction Molecular computing, known also under the name of biomolecular computing, biocomputing or DNA computing, is a new computation paradigm that employs (bio)molecule manipulation to solve computational problems. The excitement generated by the first successful experiment (Adleman 1994, [1]) was due to the fact that computing with biomolecules (mainly DNA) offered an entirely new way of performing and looking at computations: the main idea was that data could be encoded in DNA strands, and molecular biology techniques could be used to execute computational operations. Besides the novelty of the approach, molecular computing has the potential to outperform electronic computers. For example, DNA computing has the potential to provide huge memories: DNA in weak solution in one liter of water can encode 10 19 bytes, and one can perform massively parallel associative searches on these memories, [6], [42]. Computing with DNA also has the potential to supply ma
A DNA STICKER ALGORITHM FOR SOLVING NQUEEN PROBLEM *
"... Over the past few decades numerous attempts have been made to solve combinatorial optimization problems that are NPcomplete or NPhard. It has been evidenced that DNA computing can solve those problems which are currently intractable on even fastest electronic computers. This paper proposes a new D ..."
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Over the past few decades numerous attempts have been made to solve combinatorial optimization problems that are NPcomplete or NPhard. It has been evidenced that DNA computing can solve those problems which are currently intractable on even fastest electronic computers. This paper proposes a new DNA algorithm for solving NQueen problem, a complex optimization problem. The algorithm not only shows whether or not a solution exists, but provides all possible solutions by massively parallel computations. The proposed algorithm can be easily extended to solve other optimization problems. Keywords: Combinatorial optimization; NQueen problem; Molecular computing; Sticker model. 1.
DOI: 10.1080/08948550290022123 DNA Computing: Models and Implementations
"... 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.
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.