DNA algorithm for an unbounded fan-in Boolean circuit.
TL;DR: A new DNA-based evaluation algorithm for a Boolean circuit that employs standard bio-molecular techniques and is much easier to implement in the laboratory than previously described models.
Abstract: In this paper, we present a new DNA-based evaluation algorithm for a Boolean circuit that employs standard bio-molecular techniques. The algorithm operates on an unbounded fan-in Boolean circuit consisting of AND and OR gates. The whole simulation of our algorithm is proposed in a single test tube in O(1) time complexity and is much easier to implement in the laboratory than previously described models. Furthermore, the algorithm allows for evaluating any number of Boolean circuits in parallel in a single test tube.
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TL;DR: A new algorithm is formulated in this paper to design any DNA Boolean operator with molecular beacons (MBs) as its input and Boolean operators realized using the proposed design methodology is presented.
Abstract: The biological deoxyribonucleic acid (DNA) strand has been increasingly seen as a promising computing unit. A new algorithm is formulated in this paper to design any DNA Boolean operator with molecular beacons (MBs) as its input. Boolean operators realized using the proposed design methodology is presented. The developed operators adopt a uniform representation for logical 0 and 1 for any Boolean operator. The Boolean operators designed in this work employ only a hybridization operation at each stage. Further, this paper for the first time brings out the realization of a binary adder and subtractor using molecular beacons. Simulation results of the DNA-based binary adder and subtractor are given to validate the design.
13 citations
Cites background from "DNA algorithm for an unbounded fan-..."
...Ahrabian and Nowzari-Dalini (2004) and Ahrabian et al. (2005) proposed a different construction of NAND gate and the same authors presented a DNA algorithm for solving an unbounded fan-in Boolean circuit in O(1)-time complexity....
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TL;DR: The verification procedures demonstrated in this study when applied in e-voting systems would help build voter’s confidence in iVoting systems.
Abstract: The purpose of this study was to design an e-voting system to improve verification and auditing of votes and election results to aid build confidence in the use of e-voting. A top-down design approach was adopted in the design and development of the evoting system. BK Web-based e-voting system after design was implemented in ten different elections in 2012, 2013 and 2014. It was very helpful in ensuring voter’s confidence in e-voting since they were able to verify their votes through Short Message Service, reports generated from the system and the provision of ‘strong room’ facility. The verification procedures demonstrated in this study when applied in e-voting systems would help build voter’s confidence in e-voting systems.
10 citations
Cites background from "DNA algorithm for an unbounded fan-..."
...codes [Boneh et al. (1996); Leier et al. (2000)], chess problem [Faulhammer et al. (2000)], simulation of Boolean circuits [ Ahrabian et al. (2005) ; Ahrabian and Nowzari (2004); Ogihara and Ray (1999)], arithmetic and logic operation [Barua and Misra (2002); Frisco (2000); Gupta et al. (1999)], simulating Turing machine and automata [Beaver (1995); Benenson et al. (2003); Gao et al. (1999); Rothemund (1996)], and molecular expert system ......
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TL;DR: A molecular-based algorithm for evaluation of Nand-based Boolean Circuits is presented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature.
Abstract: Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.
8 citations
Cites background from "DNA algorithm for an unbounded fan-..."
...Since then, all simulation models of Boolean Circuits has been constructed by OR and AND gates([12,11,5])....
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18 Oct 2008
TL;DR: A unique generalized algorithm for forming gates with a uniform representation for logical 0 and 1 for all gates is proposed in this paper, which was not achieved in earlier works.
Abstract: The biological Deoxyribonucleic acid (DNA) strand is found to be a promising computing unit. A novel strategy is described in this paper to design any logic gates with molecular beacons (MB) as input. A unique generalized algorithm for forming gates is proposed in this paper. The implementation of the gates using the proposed algorithm and its operation are also presented. These gates require only one kind of biooperation at each level. Unlike previous techniques, this method permits having any type of gate at each level and the proposed implementation doesn't require stratification. Further, this paper adopts a uniform representation for logical 0 and 1 for all gates which was not achieved in earlier works. Simulation to validate the generalized algorithm is also presented in this work.
7 citations
Cites background or methods from "DNA algorithm for an unbounded fan-..."
...Gate strand that has been obtained from executing the above algorithm will be fixed on the surface at the 3’end[7]....
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...Arabian et al proposed a different construction of NAND gate and the same authors presented a DNA algorithm for solving an unbounded fan-in Boolean circuit in O(1)-time complexity[6, 7]....
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23 Oct 2006
TL;DR: The purpose of this paper is to explore the possibility of reliably simulating Boolean circuits using molecular beacon and present simulating an instance of bounded fan-in Boolean circuit comprising of these gates in time proportional to the depth of the circuit.
Abstract: A fundamental concept in computer science is that of the universal Turing machine, which is an abstract definition of a general purpose computer. It has also been shown that any computer which is able to simulate Boolean circuits of any complexity is such a general purpose computer. However, few studies have devoted to DNA computer of this kind. Molecular beacon is a hairpin-formed oligonucleotide probe, which can report the presence of target sequence in solution with higher specificity compared with linear probe. It is particularly useful when single base discrimination is desired in the process of hybridization underlying DNA computing. In this paper, molecular beacon is utilized to simulate logical AND and OR gates. Then we present simulating an instance of bounded fan-in Boolean circuit comprising of these gates in time proportional to the depth of the circuit. The purpose of this paper is to explore the possibility of reliably simulating Boolean circuits using Molecular Beacon.
4 citations
Cites methods from "DNA algorithm for an unbounded fan-..."
...Recently, reference [11] presented DNA algorithm for solving an unbounded fan-in Boolean circuit in ) 1 ( Ο time complexity....
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...Since the publication of Adleman’s original paper [1], various models of computation was developed using bio-molecular methods, including Turing machine [2,3], splicing systems [4], surface-based computing model [5] and Boolean circuits [6,7,8,9,10,11,12,13]....
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References
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Book•
01 Sep 1988
TL;DR: In this article, the authors present the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields, including computer programming and mathematics.
Abstract: From the Publisher:
This book brings together - in an informal and tutorial fashion - the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields
Major concepts are illustrated with running examples, and major algorithms are illustrated by Pascal computer programs No prior knowledge of GAs or genetics is assumed, and only a minimum of computer programming and mathematics background is required
52,797 citations
01 Jan 1989
TL;DR: This book brings together the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields.
Abstract: From the Publisher:
This book brings together - in an informal and tutorial fashion - the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields.
Major concepts are illustrated with running examples, and major algorithms are illustrated by Pascal computer programs. No prior knowledge of GAs or genetics is assumed, and only a minimum of computer programming and mathematics background is required.
33,034 citations
TL;DR: This experiment demonstrates the feasibility of carrying out computations at the molecular level by solving an instance of the directed Hamiltonian path problem with standard protocols and enzymes.
Abstract: The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.
4,266 citations
TL;DR: DNA experiments are proposed to solve the famous "SAT" problem of computer science and have the potential to yield vast speedups over conventional electronic-based computers for such search problems.
Abstract: DNA experiments are proposed to solve the famous "SAT" problem of computer science. This is a special case of a more general method that can solve NP-complete problems. The advantage of these results is the huge parallelism inherent in DNA-based computing. It has the potential to yield vast speedups over conventional electronic-based computers for such search problems.
1,038 citations
TL;DR: Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed and provide highly specific detection with minimal background.
Abstract: Nucleotide sequence information derived from DNA segments of the human and other genomes is accumulating rapidly. However, it frequently proves difficult to use such short DNA segments to identify clones in genomic libraries or fragments in blots of the whole genome or for in situ analysis of chromosomes. Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed. Upon recognition of the specific nucleic acid molecule the ends of the probes were joined through the action of a ligase, creating circular DNA molecules catenated to the target sequence. These probes thus provide highly specific detection with minimal background.
901 citations