Successive state transitions with I/O interface by molecules

Komiya, Ken; Sakamoto, Kensaku; Gouzu, Hidetaka; Yokoyama, Shigeyuki; Arita, Masanori; Nishikawa, Akio; Hagiya, Masami

doi:10.1007/3-540-44992-2_2

Cited by 18 publications

(10 citation statements)

References 8 publications

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“…3 All of the strong constraints could be satisfied with only 3 bases [15]. Other groups that employed three-base words likewise used random word-generation for their word design [24,23].…”

Section: Stochastic Methodsmentioning

confidence: 99%

Writing Information into DNA

Arita

2003

Aspects of Molecular Computing

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“…3 All of the strong constraints could be satisfied with only 3 bases [15]. Other groups that employed three-base words likewise used random word-generation for their word design [24,23].…”

Section: Stochastic Methodsmentioning

confidence: 99%

Writing Information into DNA

Arita

2003

Aspects of Molecular Computing

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“…Benenson, Paz-Elizur, Adar, Keinan, Livneh, and Shapiro [38] reported development of a programmable 'finite automaton', using a restriction nucleaseand ligase as hardware and software consisting of transition rules encoded by DNA. Komiya, Sakamoto, Gouzo, Yokoyama, Arita, Nishikawa, and Hagiya [39] showed that a single-stranded DNA can serve as an independent machine by using a solid support technique in three experimental achievements in computation model based on 'whiplash' reactions, while Garzon, Gao, Rose, Murphy, Deaton, Franceschetti, and Stevens [40] used a ligation-based approach for in-vitro implementation of finite-state machines, which requires sequential input feed and different molecules for different machines. In their second implementation not based on ligation transitions are represented by reusable molecules and the input, coded as a molecule, can be introduced at once.…”

Section: Dna Computation Systemsmentioning

confidence: 96%

Another expert system rule inference based on DNA molecule logic gates

Wasiewicz

2013

Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013

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With the help of silicon industry microfluidic processors were invented utilizing nano membrane valves, pumps and microreactors. These so called lab-on-a-chips combined together with molecular computing create molecular-systems-ona-chips. This work presents a new approach to implementation of molecular inference systems. It requires the unique representation of signals by DNA molecules. The main part of this work includes the concept of logic gates based on typical genetic engineering reactions. The presented method allows for constructing logic gates with many inputs and for executing them at the same quantity of elementary operations, regardless of a number of input signals. Every microreactor of the lab-on-a-chip performs one unique operation on input molecules and can be connected by dataflow output-input connections to other ones.

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“…Benenson, Paz-Elizur, Adar, Keinan, Livneh, and Shapiro [6] reported development of a programmable 'finite automaton', using a restriction nucleaseand ligase as hardware and software consisting of transition rules encoded by DNA. Komiya, Sakamoto, Gouzo, Yokoyama, Arita, Nishikawa, and Hagiya [18] showed that a single-stranded DNA can serve as an independent machine by using a solid support technique in three experimental achievements in computation model based on 'whiplash' reactions, while Garzon, Gao, Rose, Murphy, Deaton, Franceschetti, and Stevens [12] used a ligation-based approach for in-vitro implementation of finite-state machines, which requires sequential input feed and different molecules for different machines. In their second implementation not based on ligation transitions are represented by reusable molecules and the input, coded as a molecule, can be introduced at once.…”

Section: More Advanced Techniques Of Computing On Moleculesmentioning

confidence: 99%

<title>Enzyme optimization for next level molecular computing</title>

Wasiewicz¹,

Malinowski²,

Płucienniczak

2006

SPIE Proceedings

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The main concept of molecular computing depends on DNA self-assembly abilities and on modifying DNA with the help of enzymes during genetic operations. In the typical DNA computing a sequence of operations executed on DNA strings in parallel is called an algorithm, which is also determined by a model of DNA strings. This methodology is similar to the soft hardware specialized architecture driven here by heating, cooling and enzymes, especially polymerases used for copying strings. As it is described in this paper the polymerase Taq properties are changed by modifying its DNA sequence in such a way that polymerase side activities together with peptide chains, responsible for destroying amplified strings, are cut off. Thus, it introduces the next level of molecular computing. The genetic operation execution succession and the given molecule model with designed nucleotide sequences produce computation results and additionally they modify enzymes, which directly influence on the computation process. The information flow begins to circulate. Additionally, such optimized enzymes are more suitable for nanoconstruction, because they have only desired characteristics. The experiment was proposed to confirm the possibilities of the suggested implementation.

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Successive state transitions with I/O interface by molecules

Cited by 18 publications

References 8 publications

Writing Information into DNA

Writing Information into DNA

Another expert system rule inference based on DNA molecule logic gates

<title>Enzyme optimization for next level molecular computing</title>

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