PROCESSING DNA TOKENS IN PARALLEL COMPUTING

Presented by Sapnah AligetiMidwestern State University27 June 2005.

OUTLINE

• About the paper.• Define keywords.• A little about DNA.• Fundamental Operations on DNA.• History of DNA computing.• Travelling Salesman Problem.• The Experiment.• Results.• Problems.• Conclusions.• Futrue Developments.

ABOUT THE PAPER

• IEEE Proceedings in 2001• Authors

– Robert Nowak

– Piotr Wasiewicz

– Prof. Jan J.Mulawka

– Prof. Andrzej Plucienniczak

ABOUT THE PAPER (CONTD)

Abstract: In this paper a new technique of sending

data between molecular processors is presented. The molecular processor is a processing data unit. Its computation results have to be sent to other units in the form of addressed messages - tokens. Necessary experiments were performed. All operations were implemented in DNA. DNA processors and tokens were specially designed DNA strings. Results of experiments prove our assumptions.

KEYWORDS DEFINITION

• Molecular Processor.

• DNA computing.

• DNA tokens.

A LITTLE ABOUT DNA

• DNA - deoxyribonucleic acid.

A LITTLE ABOUT DNA (CONTD)

• DNA Formation

• Nucleotides– A for Adenine– T for Thymine– G for Guanine– C for Cytosine

A LITTLE ABOUT DNA (CONTD)

• DNA Structure – double helix

FUNDAMENTAL OPERATIONS ON DNA.

• Hybridization / Renaturation.• Denaturation.• Cutting.• Amplification.• Concatenation.• Extracting.

RENATURATION AND DENATURATION

DNA CUTTING.

HISTORY OF DNA COMPUTING.

• Millions of natural supercomputers exist inside living organisms.

• Sequences of A, T, G, C instead of 1’s and 0’s.

• Hamilton Path problem / Travelling salesman problem.– Discovered in 1994.– Leonard Adleman (University of

California.)

TRAVELLING SALESMAN PROBLEM.

TRAVELLING SALESMAN PROBLEM (CONTD)

• Test Tube as Computer.

• Operations are massively parallel.

TRAVELLING SALESMAN PROBLEM (CONTD)

TRAVELLING SALESMAN PROBLEM (CONTD)

• Extracting– Extract all paths having the

correct START and END.– Extract the paths with the

correct number of cities.– Extract the ones with no

repetitions of cities.– The remaining path would

be the result.

THE EXPERIMENT

DNA TOKENS ADDRESSING.

• Molecular processors in a single tube.

• Data sending by DNA tokens.

• DNA token structure.

AMPLIFICATION OF DNA

AMPLIFICATION OF DNA

RESULTS

RESULTS

PROBLEMS.

• Proper enzyme selection.– While using artificial

nucleotides.

• Extraction.

CONCLSUIONS.

• Multicast / Broadcast propagation.– Proper sequencing.

• Use of artificial nucleotide ‘N’.

FUTURE DEVELOPMENTS

• It is expected that the described molecular processor with changing states during computation will be invented in the near future and will consist of more than one DNA molecule. It is obvious that the real advantage of such systems appears during massively parallel computation. Million molecular processors could be attached with their 3’ ends to a typical DNA chip or magnetic beads placed in a microreactor. Thus, it would be the first prototype of future powerful molecular computers.

NATIONAL GEOGRAPHIC NEWS.

• February 24, 2003.

• Weizmann Institute of Science in Rehovot, Israel.

• Israeli scientists have devised a computer that can perform 330 trillion operations per second.

QUESTIONS????

THANK YOU !!!!!

EXTRA SLIDES - Gel Electrophoresis

Result of gel electrophoresis of DNA. Sequence is CGACCACCACCCCGAGGTT