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DNA Computing, Sticker Systems, and Universality
 ACTA INFORMATICA
, 1998
"... We introduce the sticker systems, a computability model, which is an abstraction of the computations using the WatsonCrick complementarity as in Adleman's DNA computing experiment, [1]. Several types of sticker systems are shown to characterize (modulo a weak coding) the regular languages, hence th ..."
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We introduce the sticker systems, a computability model, which is an abstraction of the computations using the WatsonCrick complementarity as in Adleman's DNA computing experiment, [1]. Several types of sticker systems are shown to characterize (modulo a weak coding) the regular languages, hence the power of finite automata. One variant is proven to be equivalent to Turing machines. Another one is found to have a strictly intermediate power.
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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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...
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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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...
Three Dimensional DNA Structures in Computing
 BioSystems
, 1998
"... We show that 3dimensional graph structures can be used for solving computational problems with DNA molecules. Vertex building blocks consisting of karmed (k = 3 or k = 4) branched junction molecules are used to form graphs. We present procedures for the 3SAT and 3vertexcolorability problems. Co ..."
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We show that 3dimensional graph structures can be used for solving computational problems with DNA molecules. Vertex building blocks consisting of karmed (k = 3 or k = 4) branched junction molecules are used to form graphs. We present procedures for the 3SAT and 3vertexcolorability problems. Construction of one graph structure (in many copies) is sufficient to determine the solution to the problem. In our proposed procedure for 3SAT, the number of steps required is equal to the number of variables in the formula. For the 3vertexcolorability problem, the procedure requires a constant number of steps regardless of the size of the graph. Keywords: 3dimensional structures, DNAcomputing, graphs. 1 Introduction The field of practical DNA computing opened in 1994 with Adleman's paper (1994), in which a laboratory experiment involving DNA molecules was used to solve a small instance of the Hamiltonian Path problem. In the follow up paper by Lipton (1995), it was demonstrated how a...
Fast Parallel Molecular Algorithms for DNABased Computation: Factoring Integers
"... Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two la ..."
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Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNAbased algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using publickey are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations. Index Terms—Biological parallel computing, DNAbased algorithms, DNAbased computing, factoring integers, RSA publickey cryptosystem. I.
YAC: Yet Another Computation Model of SelfAssembly
, 1999
"... . This paper proposes a new model for DNA computation termed YAC based on selfassembly principle. The model has three advantages: (i) It has the universal computability of Turing machines. (ii) It requires only simple and basic molecular biological operations. Besides annealing and melting in a o ..."
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. This paper proposes a new model for DNA computation termed YAC based on selfassembly principle. The model has three advantages: (i) It has the universal computability of Turing machines. (ii) It requires only simple and basic molecular biological operations. Besides annealing and melting in a onepot reaction, only the detection of a completely hybridized double stranded molecule is used. (iii) Therefore, a molecular biological implementation of the model seems highly feasible. In order to make YAC computation more resource efficient, we introduce an incremental computation method. 1. Introduction In recent intensive study of normal form theorems for the generative grammars in formal language theory, quite a few number of normal form theorems for a variety of types of grammars have been presented, ranging from regular grammars to phrasestructure grammars in Chomsky's hierarchy. Among others, some of the normal forms for phrasestructure grammars can be of crucially importance wh...
Information filtering based on user behaviour analysis and best match text retrieval
 Proceedings of the 17th ACM Annual International Conference on Research and Development in Information Retrieval (SIGIR'94
, 1994
"... Abstract: This paper presents the study of nanorobots control activation for stenosed coronary occlusion, with the practical use of chemical and thermal gradients for biomedical problems. The recent developments on nanotechnology new materials allied with electronics device miniaturization may enabl ..."
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Abstract: This paper presents the study of nanorobots control activation for stenosed coronary occlusion, with the practical use of chemical and thermal gradients for biomedical problems. The recent developments on nanotechnology new materials allied with electronics device miniaturization may enable nanorobots for the next few years. New possibilities for medicine are expected with the development of nanorobots. It may help to advance the treatment of a wide number of diseases: cardiovascular problems, neurosurgery, cancer, diabetes and new cell therapies. The implementation of new methodologies to help on manufacturing analyses and system design for the development of nanoscale molecular machine is one of the most important fields for research. The use of 3D physically based simulation in conjunction with clinical data may provide ways to design practical approaches for control and transducers development.
Computation = Selfassembly + Conformational Change: Toward New Computing Paradigms
 Department of Mathematics, School of Education, Waseda University
, 1999
"... . Molecular Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer scie ..."
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. Molecular Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer science (e.g., [2, 3, 7, 9, 10, 11, 13, 17, 19, 20]), trying to break through the socalled NPcompleteness barrier or to establish new computation paradigms with universal capability. This paper proposes new computing paradigms based on selfassembly and conformational change. These two principles have already appeared in an extensive variety of literature in natural science, while relatively a few studies have discussed these two together in the context of computing. In order to demonstrate a new computing schema : computation = selfassembly + conformational change, we first discuss a framework of computing model CCC (Computing by Conformational Change) by showing examples of solving several N...
Data Structures in Natural Computing: Databases as Weak or Strong Anticipatory Systems
"... Abstract. Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on t ..."
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Abstract. Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on to idealised machines with von Neumann architectures consisting of fixed instructions. Category theory developed as a formalism to explore the theoretical concept of naturality shows that methods like sketches arising from graph theory as only nonnatural models of naturality cannot capture realworld structures for strong anticipatory information systems. Databases need a schema of the natural world. Natural computing databases need the schema itself to be also natural. Natural computing methods including neural computers, evolutionary automata, molecular and nanocomputing and quantum computation have the potential to be strong. At present they are mainly at the stage of weak anticipatory systems.