DNA Computing and Errors

2011 ◽  
pp. 56-77 ◽  
Author(s):  
Lila Kari ◽  
Elena Losseva ◽  
Petr Sosik
Keyword(s):  
Computer Science ◽  
Dna Computing ◽  
Biochemical Reactions ◽  
Dna Computation ◽  
Theoretical Methods ◽  
Experimental Implementation ◽  
Algorithmic Approaches

This chapter looks at the question of managing errors that arise in DNA-based computation. Due to the inaccuracy of biochemical reactions, the experimental implementation of a DNA computation may lead to incorrectly calculated results. This chapter explores different methods that can assist in the reduction of such occurrences. The solutions to the problem of erroneous biocomputations are presented from the perspective of computer science techniques. Three main aspects of dealing with errors are covered: software simulations, algorithmic approaches, and theoretical methods. The objective of this survey is to explain how these tools can reduce errors associated with DNA computing.

scholarly journals Photochemical NOT Gate for DNA Computing

2020 ◽  
Author(s):  
Cole Emanuelson ◽  
Anirban Bardhan ◽  
Alexander Deiters
Keyword(s):  
Output Signal ◽  
Dna Computing ◽  
Logic Gates ◽  
Specific Pattern ◽  
Boolean Logic ◽  
Dna Computation ◽  
Circuit Performance ◽  
Optical Activation ◽  
Computational Circuits ◽  
Time Point

AbstractDNA-based Boolean logic gates (AND, OR and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. We developed a novel DNA gate design utilizing photocaging groups that prevents gate function until irradiation at a certain time-point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA inputs. We further demonstrate the utility of the NOT gate within multi-layer circuits in response to a specific pattern of four microRNAs.

Towards a Bio-Inspired Theoretical Linguistics to Model Man-Machine Communication

2013 ◽  
Vol 1 (1) ◽  
pp. 14-28
Author(s):  
Gemma Bel-Enguix ◽  
M. Dolores Jiménez-López
Keyword(s):  
Molecular Biology ◽  
Natural Language ◽  
Computer Science ◽  
Dna Computing ◽  
Membrane Computing ◽  
Theoretical Computer Science ◽  
Theoretical Computer ◽  
Theoretical Linguistics ◽  
Machine Communication ◽  
Natural Description

The paper provides an overview of what could be a new biological-inspired linguistics. The authors discuss some reasons for attempting a more natural description of natural language, lying on new theories of molecular biology and their formalization within the area of theoretical computer science. The authors especially explore three bio-inspired models of computation –DNA computing, membrane computing and networks of evolutionary processors (NEPs) – and their possibilities for achieving a simpler, more natural, and mathematically consistent theoretical linguistics.

scholarly journals DNA Computing: Challenges and Application

2017 ◽  
Vol 11 (2) ◽  
pp. 74 ◽  
Author(s):  
Samir Abou El-Seoud ◽  
Reham Fouad Mohamed ◽  
Samy Ghoneimy
Keyword(s):  
Dna Computing ◽  
Large Scale ◽  
Information Storage ◽  
Computational Power ◽  
Dna Computation ◽  
Fast Processing ◽  
Alternative Means ◽  
Increasing Demand ◽  
Silicon Based ◽  
Economic Future

<p class="Abstract">Much of our scientific, technological, and economic future depends on the availability of an ever-increasing supply of computational power. However, the increasing demand for such power has pushed electronic technology to the limit of physical feasibility and has raised the concern that this technology may not be able to sustain our growth in the near future. It became important to consider an alternative means of achieving computational power. In this regard, DNA computing was introduced based on the usage of DNA and molecular biology hardware instead of the typical silicon based technology. The molecular computers could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism and extraordinary energy efficiency. One of the main advantages that DNA computations would add to computation is its self - parallel processing while most of the electronic computers now use linear processing. In this paper, the DNA computation is reviewed and its state of the art challenges and applications are presented. 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. Moreover, this work focuses on whether a large scale molecular computer can be built.</p>

A ROBUST DNA COMPUTATION MODEL THAT CAPTURES PSPACE

2003 ◽  
Vol 14 (05) ◽  
pp. 933-951 ◽  
Author(s):  
EVGENY DANTSIN ◽  
ALEXANDER WOLPERT
Keyword(s):  
Dna Computing ◽  
Magnetic Beads ◽  
Computational Power ◽  
Computation Model ◽  
Dna Computation ◽  
Trade Off ◽  
Computational Problem ◽  
Complete Problems ◽  
Hard Problems ◽  
Good Trade

One of the most serious problems in DNA computing is that basic DNA operations are faulty. Many DNA computation models use operations based on annealing and magnetic-beads separation which sometimes produce undesirable results. Some models use reliable operations only but their computational power is too weak. The purpose of this paper is to find a good trade-off between the robustness of DNA operations and their computational power. We present a robust DNA computation model that can solve computationally hard problems. We prove that (i) this model can solve PSPACE-complete problems, and (ii) any computational problem that can be solved with this model is in PSPACE.

Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes

2007 ◽  
Vol 7 (2) ◽  
pp. 277-286 ◽  
Author(s):  
Zuwairie Ibrahim ◽  
John A. Rose ◽  
Akira Suyama ◽  
Marzuki Khalid
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Dna Computing ◽  
Taqman Probes ◽  
Experimental Implementation

DNA Computing Model Based on Self-Assembled Nanoparticle Probes for SAT Problem

2012 ◽  
Vol 443-444 ◽  
pp. 513-517
Author(s):  
Fei Li ◽  
Jin Xu ◽  
Zheng Li
Keyword(s):  
Dna Computing ◽  
Complex Problem ◽  
Dna Computation ◽  
Widespread Application ◽  
Sat Problem ◽  
Nanoparticle Probes ◽  
Computing Model ◽  
Model Based ◽  
Complete Problems ◽  
Self Assembled

. SAT problem is one of important NP-complete problems with widespread application. In this paper, a new DNA computing model based on self-assembled nanoparticle probes is presented to solve this problem. Its essence is that all possible combinations of variables for given problem are encoded in the recognition zone of self-assembled nanoparticle probes. Major benefits of this method include vast parallelism, extraordinary information density and easy controllable operation. The result reveals the potential of DNA computation based on nanotechnology in solving complex problem.

scholarly journals НАВЧАННЯ БАКАЛАВРІВ ІНФОРМАТИКИ З ВИКОРИСТАННЯМ МЕРЕЖНИХ ТЕХНОЛОГІЙ ВІДКРИТИХ СИСТЕМ У ПЕДАГОГІЧНОМУ УНІВЕРСИТЕТІ

2017 ◽  
Vol 58 (2) ◽  
pp. 169
Author(s):  
Tetiana Ya. Vdovychyn
Keyword(s):  
Computer Science ◽  
Open Systems ◽  
Educational Institutions ◽  
Higher Educational Institutions ◽  
Experimental Implementation ◽  
Study Results ◽  
Basic Concepts ◽  
Higher Educational ◽  
Main Components ◽  
Network Technologies

The article studies the problem of the use of open systems network technologies (OSNTs) in training of future bachelors of computer science. The theoretical principles of the use of OSNTs in higher educational institutions are defined and the basic concepts of the study are analyzed. The procedural model of the use of OSNTs in training of future bachelors of computer science is theoretically grounded and developed. The criteria, indicators and levels of competence of bachelors of computer science concerning the use of OSNTs are defined and the model of its formation is developed. The main components of OSNTs using technique for future bachelors of computer science are described and its effectiveness is experimentally verified. The experimental implementation of the study results showed that the use of OSNTs in training of bachelors of computer science based on the developed technique promotes the competence formation of bachelors of computer science concerning the use of OSNTs.

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