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Computing with Membranes
 JOURNAL OF COMPUTER AND SYSTEM SCIENCES
, 1998
"... We introduce a new computability model, of a distributed parallel type, based on the notion of a membrane structure. Such a structure consists of several celllike membranes, recurrently placed inside a unique "skin" membrane. A plane representation is a Venn diagram without intersected sets and wit ..."
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Cited by 342 (4 self)
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We introduce a new computability model, of a distributed parallel type, based on the notion of a membrane structure. Such a structure consists of several celllike membranes, recurrently placed inside a unique "skin" membrane. A plane representation is a Venn diagram without intersected sets and with a unique superset. In the regions delimited by the membranes there are placed objects; the obtained construct is called a supercell. These objects are assumed to evolve: each object can be transformed in other objects, can pas through a membrane, or can disolve the membrane in which it is placed. A priority relation between evolution rules can be considered. The evolution is done in parallel for all objects able to evolve. In this way, we obtain a computing device (we call it a supercell system): start with a certain number of objects in a certain membrane and let the system evolve; if it will halt (no object can further evolve), then the computation is finished, with the result given as...
DNA Simulation of Boolean Circuits
 Proceedings of 3rd Annual Genetic Programming Conference
, 1997
"... In this paper we describe a simulation of Boolean circuits using standard biomolecular techniques. Previously proposed simulations have been shown to run in time proportional to the size of the circuit. The simulation we present here runs in time proportional to the depth of the circuit. We describ ..."
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Cited by 25 (1 self)
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In this paper we describe a simulation of Boolean circuits using standard biomolecular techniques. Previously proposed simulations have been shown to run in time proportional to the size of the circuit. The simulation we present here runs in time proportional to the depth of the circuit. We describe the abstract model and its laboratory implementation, before concluding with a brief analysis.
DirectProportional LengthBased DNA Computing for Shortest Path Problem
 INTERNATIONAL JOURNAL OF COMPUTER SCIENCE AND APPLICATIONS
, 2004
"... Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science, and mathematics. From the DNA computing point of view, it has been proven that it is possible to solve weighted graph problems by exploiting some chara ..."
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Cited by 9 (6 self)
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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science, and mathematics. From the DNA computing point of view, it has been proven that it is possible to solve weighted graph problems by exploiting some characteristics of DNA such as length, concentration, and melting temperature. In this paper, we present an alternative directproportional lengthbased DNA computing approach whereby the cost of each path is encoded by the length of the oligonucleotides in a proportional way. The advantage is such that, after the hybridization and ligation reactions, gel electrophoresis can be performed to separate the respective DNA duplex according to their length which directly decodes the results. In addition to this advantage, the reliability of the proposed approach can be enhanced as only the general and wellknown biomolecular laboratory operations are employed during the computation.
Take Advantage of the Computing Power of DNA Computers
 In Proceedings of the Third Workshop on BioInspired Solutions to Parallel Processing Problems, IPDPS 2000 Workshops
, 2000
"... Ever since Adleman [1] solved the Hamilton Path problem using a combinatorial molecular method, many other hard computational problems have been investigated with the proposed DNA computer [3] [25] [9] [12] [19] [22] [24] [27] [29] [30]. However, these computation methods all work toward one des ..."
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Cited by 7 (0 self)
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Ever since Adleman [1] solved the Hamilton Path problem using a combinatorial molecular method, many other hard computational problems have been investigated with the proposed DNA computer [3] [25] [9] [12] [19] [22] [24] [27] [29] [30]. However, these computation methods all work toward one destination through a couple of steps based on the initial conditions. If there is a single change on these given conditions, all the procedures need to be gone through no matter how complicate these procedures are and how simple the change is. The new method we are proposing here in the paper will take care of this problem.
The Inference Based On Molecular Computing
, 2000
"... This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies ..."
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Cited by 7 (0 self)
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This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing. Series of experiments have been conducted to confirm practical utility of this approach. In these experiments, parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try to enhance physical insight into the dominating features of the approach proposed
Evolutionary Computation as a Paradigm for DNABased Computing
"... . Evolutionary Computation focuses on probabilistic search and optimization methods gleaned from the model of organic evolution. Genetic algorithms, evolution strategies and evolutionary programming are three independently developed representatives of this class of algorithms, with genetic programmi ..."
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Cited by 7 (0 self)
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. Evolutionary Computation focuses on probabilistic search and optimization methods gleaned from the model of organic evolution. Genetic algorithms, evolution strategies and evolutionary programming are three independently developed representatives of this class of algorithms, with genetic programming and classifier systems as additional paradigms in the field. This paper focuses on the link between evolutionary computation and DNAbased computing by discussing the relevant aspects of evolutionary computation both from a practical and a theoretical point of view. In particular, theoretical results concerning the calculation of convergence velocities and the derivation of optimal schedules for mutation rates respectively steps sizes are presented. The potential for crossfertilization between the fields of DNAbased computing and evolutionary computation is outlined both from a principal point of view and by means of an experimental investigation concerning the NPhard maximum clique pr...
New Computing Paradigms Suggested by DNA Computing: Computing by Carving
 4th Int. Meeting on DNABased Computing
, 1998
"... Inspired by the experiments in the emerging area of DNA computing, a somewhat unusual type of a computation strategy was recently proposed by one of us: generate a (large) set of candidate solutions of a problem, then remove the nonsolutions such that what remains is the set of solutions. This has ..."
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Cited by 5 (1 self)
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Inspired by the experiments in the emerging area of DNA computing, a somewhat unusual type of a computation strategy was recently proposed by one of us: generate a (large) set of candidate solutions of a problem, then remove the nonsolutions such that what remains is the set of solutions. This has been called a computation by carving. This idea leads both to a speculation with possible important consequences and to interesting theoretical computer science (formal language) questions. The speculation is that in this way we can "compute" nonrecursively enumerable languages, because the family of recursively enumerable languages is not closed under complementation. The formal language theory questions concern sequences of languages with certain regularities, needed as languages to be extracted from the total language of candidate solutions of a problem. Specifically, we consider sequences of languages obtained by starting from a given regular language and iteratively applying to it 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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Cited by 4 (1 self)
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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.
Towards Development on a Siliconbased Cellular Computing Machine
, 2005
"... Today’s reconfigurable technology provides vast parallelism that may be exploited in the design of a cellular computing machine. In this work a virtual Sblock FPGA is implemented on an existing FPGA, achieving not only an architecture in keeping with cellular computing principles but also suited to ..."
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Cited by 4 (1 self)
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Today’s reconfigurable technology provides vast parallelism that may be exploited in the design of a cellular computing machine. In this work a virtual Sblock FPGA is implemented on an existing FPGA, achieving not only an architecture in keeping with cellular computing principles but also suited to biologically inspired design methods. The design method proposed is a combination of evolution and development and results of running a developmental model on the cellular computing machine are presented.