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Simulating Boolean circuits on a DNA computer

Mitsunori Ogihara, Animesh Ray
1997 Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97  
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

M. Ogihara, A. Ray
1999 Algorithmica  
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

S.S. Mokri, H. Husain, W. Martono, A. Shafie
2008 American Journal of Applied Sciences  
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

Wenbin Liu, Xiaohong Shi, Shemin Zhang, Xiangrong Liu, Jin Xu
2004 Biosystems (Amsterdam. Print)  
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]

Matthew Cook and Tristan Stérin and Damien Woods
2021 arXiv   pre-print
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

B.S.E. Zoraida, Michael Arock
2010 International Journal of Computer Applications  
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]

Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
2011 Lecture Notes in Computer Science  
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

TSEREN-ONOLT ISHDORJ, ION PETRE
2008 International Journal of Foundations of Computer Science  
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  
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

B.S.E. Zoraida, Michael Arock, B.S.M. Ronald, R. Ponalagusamy
2009 Biosystems (Amsterdam. Print)  
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]

Maurice Margenstern and Pascal Mayer and Sergey Verlan
2011 arXiv   pre-print
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

Bin Shao, Xiang Liu, Dongliang Zhang, Jiayi Wu, Qi Ouyang, Ying Xu
2015 PLoS ONE  
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

J. H. Reif
2011 Science  
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

Dan Boneh, Christopher Dunworth, Richard J. Lipton, Jir̆í Sgall
1996 Discrete Applied Mathematics  
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

Moya Chen, Doris Xin, Damien Woods
2014 Natural Computing  
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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