A clocked finite state machine built from DNA

Santini, Cristina Costa; Bath, Jonathan; Tyrrell, Andy M.; Turberfield, Andrew J.

doi:10.1039/c2cc37227d

Cited by 23 publications

(16 citation statements)

References 24 publications

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“…5a. The design is based on that of Costa Santini et al 10 , but here the finite state machine is immobilized on the surface and there is no molecular clock. In our system activated dumb-bell hairpins can bind to the immobilized state machines, and the transition rule then binds to the domain formed by the conjunction of the initial state domain of the state machine and the identity domain of the hairpin gate.…”

Section: Operating a Finite State Machine Using The Dumb-bell Logic Gmentioning

confidence: 99%

“…It has been shown that 'see-saw' gates 5 can be used for thresholding and the construction of complex DNA computing systems that are capable of performing arithmetic functions 6 or demonstrating memory and inference 7 . Other DNA computing paradigms include chemical reaction networks 8 , finite state machines 9,10 or algorithmic self-assembly of tiles 11 , and it was recently demonstrated that DNA could be used to implement a non-deterministic universal Turing machine 12 . The capabilities of DNA computing machines could be broadened further via their integration with electronic systems, which could underpin new approaches for input, processing and readout 13 .…”

Section: Introductionmentioning

confidence: 99%

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Towards a bioelectronic computer: A theoretical study of a multi-layer biomolecular computing system that can process electronic inputs

Dunn

Trefzer

Johnson

et al. 2018

Preprint

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DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements have been developed, including logic gates, neural networks, finite state machines (FSMs) and nondeterministic universal Turing machines. It has also been established that DNA molecular machines can be controlled using electrical signals and that the state of DNA nanodevices can be measured using an electrochemical readout. However, to the best of our knowledge there has as yet been no demonstration of a fully integrated biomolecular computing system that has multiple levels of information processing capacity, can accept electronic inputs and is capable of independent operation. In this paper we address the question of how such a system could work. We present simulation results showing that such an integrated hybrid system could convert electrical impulses into biomolecular signals, perform logical operations and take a decision, storing its history. We also illustrate theoretically how such a system could potentially be used to perform a task such as controlling an autonomous robot navigating through a maze.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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Section: Operating a Finite State Machine Using The Dumb-bell Logic Gmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Towards a bioelectronic computer: A theoretical study of a multi-layer biomolecular computing system that can process electronic inputs

Dunn

Trefzer

Johnson

et al. 2018

Preprint

Self Cite

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show abstract

“…It has been shown that ‘see-saw’ gates [ 18 ] can be used for thresholding and the construction of complex DNA computing systems that are capable of performing arithmetic functions [ 19 ] or demonstrating memory and inference [ 20 ]. Other DNA computing paradigms include chemical reaction networks [ 21 ], finite state machines [ 22 , 23 ] or algorithmic self-assembly of tiles [ 24 ], and it was recently demonstrated that DNA could be used to implement a non-deterministic universal Turing machine [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Towards a Bioelectronic Computer: A Theoretical Study of a Multi-Layer Biomolecular Computing System That Can Process Electronic Inputs

Dunn

Trefzer

Johnson

et al. 2018

IJMS

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DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements have been developed, including logic gates, neural networks, finite state machines (FSMs) and non-deterministic universal Turing machines. DNA molecular machines can be controlled using electrical signals and the state of DNA nanodevices can be measured using electrochemical means. However, to the best of our knowledge there has as yet been no demonstration of a fully integrated biomolecular computing system that has multiple levels of information processing capacity, can accept electronic inputs and is capable of independent operation. Here we address the question of how such a system could work. We present simulation results showing that such an integrated hybrid system could convert electrical impulses into biomolecular signals, perform logical operations and take a decision, storing its history. We also illustrate theoretically how the system might be able to control an autonomous robot navigating through a maze. Our results suggest that a system of the proposed type is technically possible but for practical applications significant advances would be required to increase its speed.

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“…Besides, only a few of transition metal complexes containing bis(5-methyl-1H-pyrazole-3-carboxylic acid)alkane ligands have been reported. [21][22][23] (3, 2D) and [Pb(L 2 )(2,2'-bpy)] 2n ·9nH 2 O (4, 1D) were isolated therefrom. In this paper, the synthesis, crystal structures and luminescent properties of the compounds 1-5 were described.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and Structural Diversity of Main Group Metal Coordination Complexes Constructed from V‐Shape Bis(3‐methyl‐1H‐pyrazole‐4‐carboxylic acid)alkane Ligands

Cheng¹,

Bao²,

Wu³

et al. 2018

ChemistrySelect

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Reaction of H2L1/H2L2/H2L3 with corresponding main group metal salts generated five complexes, [Mg(L1)(phen)(H2O)3]⋅5H2O (1, mononuclear), [Sr(CH3OH)(L1)2Sr(H2O)2]2n⋅nH2O (2, 2D), [Ba(L2)(H2O)3]n (3, 2D), [Pb(L2)(2,2′‐bpy)]2n⋅9nH2O (4, 1D) and [Pb(L3)(phen)]2⋅2DMF (5, dinuclear) (H2L1=1,1'‐methylenebis(5‐methyl‐pyrazole‐4‐carboxylic acid, H2L2 = 2'‐methylenebis(3‐methyl‐pyrazole‐4‐carboxylic acid, H2L3=1,1'‐methylenebis(3‐methyl‐pyrazole‐4‐carboxylic acid; 2,2’‐bpy=2,2′‐bpyridine and phen=1,10‐phenanthroline). In the zwitterionic complex 1, a loop‐loop water‐water hydrogen bonded chain presented in the 3D supramolecular network, which was constructed by π⋅⋅⋅π interactions and hydrogen bonds. In CPs 2 and 3, the 1D inorganic M–O–M connectivity was built from Sr2O16 and BaO9 polyhedra, respectively. The similar 24‐membered Pb2(L2)2/Pb2(L3)2 macrocycle occurred in both 1D polymer 4 and dinuclear complex 5, with two 2,2’‐bpy molecules located inside or two phen molecules outside each macrocycle respectively. The thermal and photoluminescent properties of 1–5 in the solid state have also been investigated.

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A clocked finite state machine built from DNA

Cited by 23 publications

References 24 publications

Towards a bioelectronic computer: A theoretical study of a multi-layer biomolecular computing system that can process electronic inputs

Towards a bioelectronic computer: A theoretical study of a multi-layer biomolecular computing system that can process electronic inputs

Towards a Bioelectronic Computer: A Theoretical Study of a Multi-Layer Biomolecular Computing System That Can Process Electronic Inputs

Synthesis and Structural Diversity of Main Group Metal Coordination Complexes Constructed from V‐Shape Bis(3‐methyl‐1H‐pyrazole‐4‐carboxylic acid)alkane Ligands

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