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Simulating Boolean circuits on a DNA computer
1997
Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97
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We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. ...
Boolean circuits embody the notion of massively parallel signal processing and are jrequen,tly encountered in many parallel algorithms. Many important problems such as sorting, integer arith- ...
This paper shows that DNA chemistry allows one to simulate large semi-unbounded janin Boolean circuits with a logarithmic slowdown in computation time. ...
doi:10.1145/267521.267759
dblp:conf/recomb/OgiharaR97
fatcat:gs7jphlw7jh3zlkqcpxpryvh7m
Simulating Boolean Circuits on a DNA Computer
1999
Algorithmica
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We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. ...
Boolean circuits embody the notion of massively parallel signal processing and are jrequen,tly encountered in many parallel algorithms. Many important problems such as sorting, integer arith- ...
This paper shows that DNA chemistry allows one to simulate large semi-unbounded janin Boolean circuits with a logarithmic slowdown in computation time. ...
doi:10.1007/pl00008276
fatcat:p3pzr3kp2zgalg56gcduyvz644
Real Time Implementation of NARMA-L2 Control of a Single Link Manipulator
2008
American Journal of Applied Sciences
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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. ...
NAND-BASED BOOLEAN CIRCUIT In this study the simulation model has been proposed based on a Boolean circuit with the following specification [4] : An n-input, m-input Boolean circuit is modeled as a directed ...
doi:10.3844/ajassp.2008.1758.1763
fatcat:3rp2oxgopvduff64otu44zwxh4
A new DNA computing model for the NAND gate based on induced hairpin formation
2004
Biosystems (Amsterdam. Print)
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In this contribution, we present a theoretical model for the logical NAND gate based on induced hairpin formation. ...
Hairpin structure of DNA molecules has been widely employed in a variety of biosensors and in nanoscale molecular assembly applications. ...
In an effort to seek potential applications where DNA computers can outperform silicon-based counterparts, Ogihara and Ray (1999) first proposed to simulate Boolean circuits by DNA molecules. ...
doi:10.1016/j.biosystems.2004.04.005
pmid:15527948
fatcat:hkmdns5nsbestcyfvhtshfccf4
Small tile sets that compute while solving mazes
[article]
2021
arXiv
pre-print
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The model has a number of implementation prospects, one being DNA strands that attach to a DNA origami substrate. ...
The first has four tiles and simulates Boolean circuits by directly implementing NAND, NXOR and NOT gates. ...
Acknowledgements We thank Trent Rogers, Niall Murphy, Pierre Marcus and Nicolas Schabanel for useful discussions on the Maze-Walking Tile Assembly Model. ...
arXiv:2106.12341v1
fatcat:vn2r2tyojnelpecbzuxkykxffu
An Efficient Algorithm for Constructing DNA Boolean Circuit
2010
International Journal of Computer Applications
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Computation using biological Deoxyribonucleic acid (DNA) strand is increasingly found to be a viable proposition. ...
This Boolean circuit requires only one kind of bio-operation at each level. Further, this paper adopts a uniform representation for logical 0 and 1 for all Boolean circuit. ...
Amos et al described the simulation of a bounded fan-in Boolean circuit with NAND gate, which takes time proportional to the depth of the circuit for computation. ...
doi:10.5120/524-684
fatcat:c5f5zpjuxbdwblss2esc5bii2u
Localized Hybridization Circuits
[chapter]
2011
Lecture Notes in Computer Science
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We also use the Visual DSD simulation software in conjunction with localized reaction rates to simulate a localized circuit for computing the square root of a four bit number. ...
The circuits act via enzyme-free DNA hybridization reaction cascades. Our designs include composable OR, AND and propagation Boolean gates, and techniques to achieve higher degree fan-in and fan-out. ...
We would also like to thank Sudhanshu Garg for assisting in creating figures for a preliminary draft and Archana Ramamoorthy for proof-reading. ...
doi:10.1007/978-3-642-23638-9_8
fatcat:hw26hugsavebncqj4dmynkwgsi
GENE ASSEMBLY MODELS AND BOOLEAN CIRCUITS
2008
International Journal of Foundations of Computer Science
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We propose two different ways to simulate Boolean circuits in the framework of ciliate computations, based on the intramolecular and on the intermolecular gene assembly models with contextual operations ...
In both cases, the running time and the size of resources of the simulating devices are proportional to the corresponding depth and size of the simulated Boolean circuits. ...
There are several bio-experimental and theoretical algorithms of simulating Boolean gates and circuits in the literature, based, e.g., on DNA and membrane computing, see [14, 3, 7] . ...
doi:10.1142/s0129054108006182
fatcat:5eqoeqfivfhjvlyilkceqnnflu
Page 3612 of Mathematical Reviews Vol. , Issue 2000e
[page]
2000
Mathematical Reviews
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Summary: “We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. ...
[Ray, Animesh] (1-RCT-B; Rochester, NY)
Simulating Boolean circuits on a DNA computer. (English summary)
Algorithmica 25 (1999), no. 2-3, 239-250. ...
A novel generalized design methodology and realization of Boolean operations using DNA
2009
Biosystems (Amsterdam. Print)
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The biological deoxyribonucleic acid (DNA) strand has been increasingly seen as a promising computing unit. ...
Simulation results of the DNA-based binary adder and subtractor are given to validate the design. ...
Amos and Dunne (1997) described the simulation of a bounded fan-in Boolean circuit with NAND gate, which takes time proportional to the depth of the circuit for computation. ...
doi:10.1016/j.biosystems.2009.05.010
pmid:19505531
fatcat:x5ihdqr43fcrdlgsiuf4mxmiti
DNA Circuits Based on Isothermal Constrained Loop Extension DNA Amplification
[article]
2011
arXiv
pre-print
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We then explain how to introduce negation, which allows us to prove that, in principle, it is possible to implement the computation of any boolean function on DNA strands using ICLEDA. ...
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification ( ...
For a boolean formula φ such a modified circuit can be constructed by a superposition of two circuits, one computing φ and the other one computing ¬φ. ...
arXiv:1105.1424v1
fatcat:grczo5r7cvb4hiegzdknrlida4
From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits
2015
PLoS ONE
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Computational circuit design with desired functions in a living cell is a challenging task in synthetic biology. ...
In the first step, the search space of possible topologies for target functions is reduced by reverse engineering using a Boolean network model. ...
Here, we focus on one critical biological behavior, the SOS response in E. coli., wherein DNA repair is induced in response to the existence of a single stranded DNA (ssDNA). ...
doi:10.1371/journal.pone.0128630
pmid:26061094
pmcid:PMC4464762
fatcat:3rgfw4huavapjgzgakkott6hbm
Scaling Up DNA Computation
2011
Science
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The ability to evaluate a Boolean circuit with multiple Boolean gates pro-vides universal computation power, because any digital computation can be executed by Boolean circuit evaluation. ...
Qian and Winfree executed a seesaw circuit computation simultaneously on a vast number (trillions) of DNA molecules within a test tube, whereas biological regulatory circuits make use of relatively small ...
This prolifi c activity hints at a tortured inner structure. On page 1186 of this issue, Khurana et al. ...
doi:10.1126/science.1208068
pmid:21636761
fatcat:vfjfbhwefvcaddn4crrqjmtruu
On the computational power of DNA
1996
Discrete Applied Mathematics
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We show how DNA-based computers can be used to solve the satisfiability problem for boolean circuits. ...
Furthermore, we show how DNA computers can solve optimization problems directly without first solving several decision problems. Our methods also enable random sampling of satisfying assignments. ...
Table 1 describes the results on simulation of various classical computational models using DNA computation. ...
doi:10.1016/s0166-218x(96)00058-3
fatcat:dosq2tnxpnf5pifyspijgcigr4
Parallel computation using active self-assembly
2014
Natural Computing
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We show that nubots is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time. ...
Circuit depth is a well-studied notion of parallel time, and our result implies that nubots is a highly parallel model of computation in a formal sense. ...
on circuit complexity theory. ...
doi:10.1007/s11047-014-9432-y
fatcat:u42hmjn5bnaodovonadffeiei4
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