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Optically programming DNA computing in microflow reactors

John S. McCaskill
2001 Biosystems (Amsterdam. Print)  
The specific problem is encoded in an initial labeling pattern of each module with one of 2N DNA oligonucleotides, identical for all instances of maximal clique.  ...  Thirdly, a method for optically programming the DNA labeling process via photochemical lithography is proposed, allowing different problem instances to be specified.  ...  Acknowledgements The author would like to thank R. Penchovsky and D. van Noort for a careful reading of the manuscript.  ... 
doi:10.1016/s0303-2647(01)00099-5 pmid:11267740 fatcat:ewyjbpdzdjhlnfcmugk2rhsepy

Ligation module for in vitro selection in DNA computing

Danny van Noort, In-Hee Lee, Laura F. Landweber, Byoung-Tak Zhang, Dan V. Nicolau
2005 Biomedical Applications of Micro- and Nanoengineering II  
In this paper a classical AI problem is proposed to be solved by DNA computing: theorem proving.  ...  Since the complexity grows exponentially with the size of the problem, the solving process should be done in parallel. Massive parallelism is one of the advantages of DNA computers.  ...  Furthermore the support from the Molecular Evolutionary Computing (MEC) project of the Korean Ministry of Commerce, Industry and Energy, and the National Research Laboratory (NRL) Program from the Korean  ... 
doi:10.1117/12.582210 fatcat:pqkb34ddkfaglbfrdkdl5zf3wi

DNA Computing in Microreactors [chapter]

Danny van Noort, Frank-Ulrich Gast, John S. McCaskill
2002 Lecture Notes in Computer Science  
This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem.  ...  The goal of this research is to improve the programmability of DNA-based computers.  ...  Acknowledgement The authors wish to acknowledge the support of the GMD for DNA computing and the German Ministry of Science (BMBF) for BioMIP's start-up grant (#01SF9952).  ... 
doi:10.1007/3-540-48017-x_4 fatcat:rvwodb3l6fft3on4wffjnl6m3u

DNA computing in microreactors

Patrick Wagler, Danny van Noort, John S. McCaskill, Laszlo B. Kish, Erol C. Harvey, William B. Spillman, Jr.
2001 BioMEMS and Smart Nanostructures  
This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem.  ...  The goal of this research is to improve the programmability of DNA-based computers.  ...  Acknowledgement The authors wish to acknowledge the support of the GMD for DNA computing and the German Ministry of Science (BMBF) for BioMIP's start-up grant (#01SF9952).  ... 
doi:10.1117/12.454623 fatcat:qwg7zryacfhexotsgnjjyu5or4

DNA Computing: A Complete Overview

2016 International Journal of Science and Research (IJSR)  
DNA computing is a nascent technology that seeks to capitalize on the enormous informational capacity of DNA, biological molecules that can store huge amounts of information and are able to perform operations  ...  Computers made of genes' building blocks. Because of their speed, miniaturization and Data Storage potential DNA computers are being considered as a replacement for silicon-based computers.  ...  He also demonstrated how DNA computing solves a two variable SAT problem. Lipton proposed a solution to the SAT. The proposed DNA algorithm can solve an n-variable m-clause SAT problem in m steps.  ... 
doi:10.21275/v5i1.nov152943 fatcat:hylmrplbdreifigzdaj6knczyy

DNA Computing: Challenges and Application

Samir Abou El-Seoud, Reham Fouad Mohamed, Samy Ghoneimy
2017 International Journal of Interactive Mobile Technologies  
Some of these applications are those require fast processing, at which DNA computers would be able to solve the hardest problems faster than the traditional ones.  ...  For example, 10 trillion DNA molecules can fit in one cubic centimeter that would result in a computer that holds 10 terabytes of data.  ...  A "knight problem" with the condition that the knights must not attack each other on a 3 ! 3 chessboard was interpreted as an SAT problem using DNA (Faulhammer, et al 2000) .  ... 
doi:10.3991/ijim.v11i2.6564 fatcat:ozsmi3yhlrdepl2ooducsnsppy

Soft magnetic tweezers: A proof of principle

Francesco Mosconi, Jean François Allemand, Vincent Croquette
2011 Review of Scientific Instruments  
Finally, we propose a simple way to modify the experimental design of electromagnets that should bring the performances of the device to a competitive level.  ...  They take advantage of a nonlinear coupling regime that appears when a fast rotating magnetic field is applied to a superparamagnetic bead immersed in a viscous fluid.  ...  ACKNOWLEDGMENTS 814 The authors would like to thank David Bensimon, 815 Charlie Gosse, and Giovanni Cappello for precious discussion 816 and suggestions.  ... 
doi:10.1063/1.3531959 pmid:21456769 fatcat:cgihi34svbgb3mofy5ju34nlui

A Surface-Based Approach to DNA Computation

LLOYD M. SMITH, ROBERT M. CORN, ANNE E. CONDON, MAX G. LAGALLY, ANTHONY G. FRUTOS, QINGHUA LIU, ANDREW J. THIEL
1998 Journal of Computational Biology  
A simple, surface-based model of computation is described and it is shown how to implement an exhaustive search algorithm for the SAT problem on this model.  ...  A new model of DNA-based computation is presented. The main di erence between this model and that of Adleman is in manipulation of DNA strands that are rst immobilized on a surface.  ...  Their work has led to hopes of a DNA computer that can outperform the fastest realizable super computers at such problems.  ... 
doi:10.1089/cmb.1998.5.255 pmid:9672831 fatcat:xlal3c6iczf63m3hsffx7cvud4

Formal Verification of Molecular Computational Models in ACL2: A Case Study [chapter]

Francisco J. Martín-Mateos, José A. Alonso, Maria José Hidalgo, José Luis Ruiz-Reina
2004 Lecture Notes in Computer Science  
Theorem proving is a classical AI problem with a broad range of applications.  ...  Since its complexity is exponential in the size of the problem, many methods to parallelize the process has been proposed.  ...  We have presented a recursive formalization, in opposite to the iterative version presented in [14] . This fact is due to the applicative nature of ACL2.  ... 
doi:10.1007/978-3-540-25945-9_34 fatcat:ejnq7yyyo5etlpy4wp4wp3frrq

New field of cryptography: DNA cryptography

Guozhen Xiao, Mingxin Lu, Lei Qin, Xuejia Lai
2006 Science Bulletin  
Acknowledgements This work was supported by the National Natural Science Foundation of China (Grant No. 60473028). We thank the review experts for their very valued revise advice.  ...  The computing model proposed by Adleman is also used by Lipton to solve SAT problems [17] .  ...  In 2002, a team led by Adleman solved a 3-SAT problem with more than 1 million possibilities on a simple DNA computer after an exhaustive searching [13] .  ... 
doi:10.1007/s11434-006-2012-5 fatcat:wjh73wmrgzdvlmdfruq5ia6kfi

DNA Library Design for Molecular Computation

Robert Penchovsky, Jörg Ackermann
2003 Journal of Computational Biology  
It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules.  ...  The approach takes into account the ability of DNA strands to hybridize in complex structures like hairpins, internal loops, or bulge loops and computes the stability of the hybrids formed based on thermodynamic  ...  (Detroit, USA) for permission to use his DNA energy parameters.  ... 
doi:10.1089/106652703321825973 pmid:12804092 fatcat:44vid2vm3baipp4etxo2sho2zq

Computing with DNA

L Kari, L F Landweber
2000 Msphere  
The most recent attempt to break down these barriers is to replace, once more, the tools for performing computations with biological ones instead of electrical ones.  ...  DNA computing (also sometimes referred to as biomolecular computing or molecular computing) is a new computational paradigm that employs (bio)molecule manipulation to solve computational problems, at the  ...  A Formal Model for DNA Computing and its Computational Power One aspect of theoretical research on DNA computing is the search for a suitable formal model to describe molecular computations.  ... 
pmid:10547850 fatcat:kdccyasr2baezknjmefmzq2ynq

DNA computing on surfaces

Qinghua Liu, Liman Wang, Anthony G. Frutos, Anne E. Condon, Robert M. Corn, Lloyd M. Smith
2000 Nature  
Correspondence and requests for materials should be addressed to L.F.C. (e-mail:chi@nwz.uni-muenster.  ...  surfaces. 25 DNA computing was proposed 1 as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the`NP-complete' or  ...  All methods for solving the SAT problem (on any realizable computing device) that have been analysed require a number of steps that grows exponentially with the number of variables.  ... 
doi:10.1038/35003155 pmid:10646598 fatcat:uyx3bwgiubgslp5unooj6srf5a

Something has to give: scaling combinatorial computing by biological agents exploring physical networks encoding NP-complete problems

Falco C. M. J. M. van Delft, Giulia Ipolitti, Dan V. Nicolau, Ayyappasamy Sudalaiyadum Perumal, Ondřej Kašpar, Sara Kheireddine, Sebastian Wachsmann-Hogiu, Dan V. Nicolau
2018 Interface Focus  
On-chip network-based computation, using biological agents, is a new hardware-embedded approach which attempts to find solutions to combinatorial problems, in principle, in a shorter time than the fast  ...  Given the brute force approach of network-based systems for solving a problem of input size C, 2C solutions must be visited.  ...  However, the alternative computation approaches, including DNA, quantum, and networks-based computing, to name a few, propose in the first instance computing devices with associated operational procedures  ... 
doi:10.1098/rsfs.2018.0034 pmid:30443332 pmcid:PMC6227808 fatcat:3gl3whrp45ezloxjxf7jawfamu

Solution of a 20-Variable 3-SAT Problem on a DNA Computer

R. S. Braich
2002 Science  
A 20-variable instance of the NP-complete three-satisfiability (3-SAT ) problem was solved on a simple DNA computer.  ...  Problems of this size appear to be beyond the normal range of unaided human computation.  ...  A 20-variable instance of a 3-SAT problem was solved using (except during input and output) DNA Watson-Crick pairing and melting as the sole "operation."  ... 
doi:10.1126/science.1069528 pmid:11896237 fatcat:ljrgzpq7gvh5bdvkz3iv5moiky
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