The inference via DNA computing

Wasiewicz, Piotr; Janczak, T.; Mulawka, Jan J.; Płucienniczak, Andrzej

doi:10.1109/cec.1999.782530

Cited by 15 publications

(18 citation statements)

References 7 publications

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“…Since Adleman's first experiment [1], many researchers utilized parallel reactions of DNA molecules to solve hard computational problems [3,7,17]. Recently, several research groups have proposed DNA computing methods for logical reasoning [6,10,16,15].…”

Section: Introductionmentioning

confidence: 99%

“…Wasiewicz et al [16] describe an inference system using molecular computing. Their inference system is different from ours in that theirs does not use a resolution refutation technique.…”

Section: Introductionmentioning

confidence: 99%

“…But his suggestion is not physically feasible, because it requires too many experimental steps. Except for the inference system in [16], none of these was implemented in real bio-lab experiments.…”

Section: Introductionmentioning

confidence: 99%

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DNA Implementation of Theorem Proving with Resolution Refutation in Propositional Logic

et al. 2003

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Abstract. Theorem proving is a classical AI problem having a broad range of applications. Since its complexity grows exponentially with the size of the problem, many researchers have proposed methods to parallelize the theorem proving process. In this paper, we use the massive parallelism of molecular reactions to implement parallel theorem provers. In particular, we show that the resolution refutation proof procedure can be naturally and efficiently implemented by DNA hybridization. Novel DNA encoding schemes, i.e. linear encoding and hairpin encoding, are presented and their effectiveness is verified by bio-lab experiments.

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Section: Introductionmentioning

confidence: 99%

“…Wasiewicz et al [16] describe an inference system using molecular computing. Their inference system is different from ours in that theirs does not use a resolution refutation technique.…”

Section: Introductionmentioning

confidence: 99%

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DNA Implementation of Theorem Proving with Resolution Refutation in Propositional Logic

et al. 2003

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“…Biomolecular implementations of finite automata 8,9 and logic gates 4,10-13 have already been developed [14][15][16][17][18] . Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions.…”

mentioning

confidence: 99%

“…Logic programming has applications in artificial intelligence research 22 , natural language processing 23,24 and concurrent programming 25 . Logic programming inspired several designs for DNA-based inference systems 14,15,17,18 , including an example of laboratory-scale DNA computing with a human-assisted protocol 16 . These implementations of propositional logic programs were considered a stepping stone to predicate logic, which has the computation power of a Turing machine 26,27 .…”

mentioning

confidence: 99%

Molecular implementation of simple logic programs

2009

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Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications [1][2][3][4][5][6][7] . Biomolecular implementations of finite automata 8,9 and logic gates 4,10-13 have already been developed [14][15][16][17][18] . Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision 2,4,8,9,11,12,19 . A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.Our logic system consists of propositions, implications and queries, represented by short DNA molecules, some single-stranded and some double-stranded, as shown in Fig. 1a. A proposition p, such as 'Socrates is a Man', is represented by a double-stranded (ds) DNA molecule with a sticky end representing p on one end and a fluorophore (a fluorescent molecule) with a matching quencher (a molecule that absorbs excitation energy from a fluorophore) at its other end. A query p?, such as 'Is Socrates a Man?', is represented by a dsDNA molecule with a sticky end complementary to the representation of p and a recognition site (marked light red) for the restriction enzyme FokI. A molecular query p? can be positively answered by the molecular proposition p, because they have complementary sticky ends, as shown in Fig. 1b. The sticky end of the query molecule q? hybridizes with that of the proposition molecule q. FokI is attracted to its recognition site on the query (before hybridization or possibly following it) and cleaves the proposition molecule q. This results in the separation of its remaining sense and antisense strands, which in turn abolishes the quenching of the green fluorophore, allowing the fluorophore to emit green light in response to light excitation. This green emission can be interpreted by an outside observer as a positive response to the query.An implication p q (for example 'Socrates is Mortal if Socrates is a Man') is represented by a hairpin single-stranded (ss) DNA with three components: a sticky end representing the proposition p, a segment complementary to the representation of q and a segment that together with an auxiliary complementary strand forms a recognition site for FokI. The implication p q can be used to reduce the query p? to the query q?, meaning that to positively answer p? it suffices to positively answer q? This query reduction is justified by the d...

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A DNA Coding Scheme for Searching Stable Solutions

Kim

Lian

Kang

2005

Lecture Notes in Computer Science

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Abstract. This paper presents a novel method for searching stable solutions using a DNA coding scheme. Often there is more than one solution that satisfies the system requirements. These solutions can be viewed as extremes in the multimodal function. All extremes are not the same in that some of them are sensitive to noise or perturbation. This paper addresses the method that selects a solution that meets the system requirements in terms of output performance and is tolerant to the perspective noise or perturbation. A new method called a gradient DNA Coding is proposed to achieve such objectives. A numerical example is presented and comparing DNA coding with genetic algorithm is also given.

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The inference via DNA computing

Cited by 15 publications

References 7 publications

DNA Implementation of Theorem Proving with Resolution Refutation in Propositional Logic

DNA Implementation of Theorem Proving with Resolution Refutation in Propositional Logic

Molecular implementation of simple logic programs

A DNA Coding Scheme for Searching Stable Solutions

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